Mercurial > repos > bgruening > diffbind
annotate diffbind.xml @ 16:163688bb8f73 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 77828512472bf9815bdda725a58a2321f7803661"
author | iuc |
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date | Wed, 18 Nov 2020 12:54:07 +0000 |
parents | 194e3f2c1d86 |
children | 2605cbdaa7d8 |
rev | line source |
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16
163688bb8f73
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 77828512472bf9815bdda725a58a2321f7803661"
iuc
parents:
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diff
changeset
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1 <tool id="diffbind" name="DiffBind" version="2.10.0+galaxy0"> |
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6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
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2 <description> differential binding analysis of ChIP-Seq peak data</description> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
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3 <requirements> |
15
194e3f2c1d86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 515da67fc6c289aa7ea75a0819b5da3a902f87a2
iuc
parents:
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diff
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4 <requirement type="package" version="2.10.0">bioconductor-diffbind</requirement> |
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163688bb8f73
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 77828512472bf9815bdda725a58a2321f7803661"
iuc
parents:
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diff
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5 <requirement type="package" version="3.5.1">r-base</requirement> |
15
194e3f2c1d86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 515da67fc6c289aa7ea75a0819b5da3a902f87a2
iuc
parents:
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6 <requirement type="package" version="1.20.3">r-getopt</requirement> |
194e3f2c1d86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 515da67fc6c289aa7ea75a0819b5da3a902f87a2
iuc
parents:
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7 <requirement type="package" version="0.2.20">r-rjson</requirement> |
9
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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changeset
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8 </requirements> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
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9 <stdio> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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10 <regex match="Execution halted" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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11 source="both" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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12 level="fatal" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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13 description="Execution halted." /> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
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14 <regex match="Input-Error 01" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
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15 source="both" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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16 level="fatal" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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17 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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18 <regex match="Error in" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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19 source="both" |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff
changeset
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20 level="fatal" |
12
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
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21 description="An undefined error occured, please check your input carefully and contact your administrator." /> |
9
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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changeset
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22 </stdio> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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23 <version_command><![CDATA[ |
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4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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24 echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
9
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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25 ]]></version_command> |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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26 <command><![CDATA[ |
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4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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27 #import re |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
10
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28 #import json |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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29 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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30 ## Adapted from DESeq2 wrapper |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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31 #set $temp_factor_names = list() |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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32 #set $temp_factor = list() |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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33 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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34 #for $g in $rep_group: |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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35 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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36 #set $peak_files = list() |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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37 #set $bam_files = list() |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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38 #set $bam_controls = list() |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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39 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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40 #for $file in $g.peaks: |
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c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
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41 #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed" |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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42 ln -s '${file}' '${file_name}' && |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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43 $peak_files.append($file_name) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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44 #end for |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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45 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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46 #for $bam in $g.bamreads: |
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c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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47 #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier)) |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
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48 #set $bam_file = $bam_name + "-bamreads.bam" |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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49 #set $bam_index = $bam_name + "-bamreads.bai" |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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50 ln -s '${bam}' '${bam_file}' && |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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51 ln -s '${bam.metadata.bam_index}' '${bam_index}' && |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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52 $bam_files.append($bam_file) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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53 #end for |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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54 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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55 $temp_factor.append( {str($g.groupName): $peak_files} ) |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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56 $temp_factor.append( {str($g.groupName): $bam_files} ) |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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57 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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58 #if str( $g.bamcontrol ) != 'None': |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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59 #for $ctrl in $g.bamcontrol: |
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c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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60 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier)) |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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61 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam" |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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62 #set ctrl_index = $ctrl_name + "-bamcontrol.bai" |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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63 #if $ctrl_file not in json.dumps($temp_factor): |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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64 ln -s '${ctrl}' '${ctrl_file}' && |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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65 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' && |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
parents:
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66 #end if |
c97a786e8fb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
iuc
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67 $bam_controls.append($ctrl_file) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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68 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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69 $temp_factor.append( {str($g.groupName): $bam_controls} ) |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
parents:
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70 #end if |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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71 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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72 #end for |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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73 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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74 $temp_factor.reverse() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
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75 $temp_factor_names.append(["Condition", $temp_factor]) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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76 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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77 |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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78 Rscript '$__tool_directory__/diffbind.R' |
4c7ab9995f9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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79 |
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80 -i '#echo json.dumps(temp_factor_names)#' |
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81 -o '$outfile' |
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82 -t $th |
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83 -f $out.format |
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84 -p '$plots' |
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85 |
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86 #if $scorecol: |
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87 -n "$scorecol" |
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88 #end if |
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89 #if $lowerbetter: |
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90 -l "$lowerbetter" |
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91 #end if |
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92 #if $summits: |
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93 -s "$summits" |
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94 #end if |
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95 |
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96 #if $out.binding_matrix: |
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97 -b |
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98 #end if |
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99 |
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100 #if $out.rdata: |
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101 -r |
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102 #end if |
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103 |
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104 #if $out.analysis_info: |
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105 -a |
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106 #end if |
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107 |
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108 #if $out.rscript: |
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109 && cp '$__tool_directory__/diffbind.R' '$rscript' |
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110 #end if |
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111 ]]> |
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112 </command> |
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113 <inputs> |
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114 <repeat name="rep_group" title="Group" min="2" max="2" default="2"> |
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115 <param name="groupName" type="text" label="Name" |
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116 help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores."> |
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117 <sanitizer> |
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118 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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119 </sanitizer> |
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120 <validator type="empty_field" /> |
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121 </param> |
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122 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/> |
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123 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM files" help="Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files."/> |
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124 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM files" help="If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files."/> |
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125 </repeat> |
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126 |
12
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127 <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)"> |
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128 <sanitizer> |
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129 <valid initial="string.digits"/> |
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130 </sanitizer> |
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131 </param> |
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132 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" /> |
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133 <param name="summits" type="integer" min="0" optional="True" label="Summits" help="Extend peaks Nbp up- and downstream of the summit. For punctate peaks it is advisable to extend (e.g. 250bp), see the DiffBind User Guide"> |
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134 <sanitizer> |
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135 <valid initial="string.digits"/> |
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136 </sanitizer> |
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137 </param> |
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138 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/> |
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139 |
10
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140 <!-- Output Options --> |
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141 <section name="out" expanded="false" title="Output Options"> |
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142 <param name="format" type="select" label="Output Format"> |
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143 <option value="interval" selected="True">Interval</option> |
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144 <option value="bed">BED</option> |
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145 <option value="tabular">Tabular (tab-separated)</option> |
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146 </param> |
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147 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" /> |
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148 <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" /> |
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149 <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"/> |
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150 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/> |
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151 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/> |
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152 </section> |
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153 </inputs> |
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154 |
9
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155 <outputs> |
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156 <data name="outfile" format="interval" label="${tool.name} on ${on_string}: Differentially bound sites"> |
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157 <change_format> |
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158 <when input="out.format" value="bed" format="bed" /> |
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159 <when input="out.format" value="tabular" format="tabular" /> |
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160 </change_format> |
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161 </data> |
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162 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots"> |
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163 <filter>out['pdf']</filter> |
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164 </data> |
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165 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix"> |
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166 <filter>out['binding_matrix']</filter> |
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167 </data> |
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168 <data name="rdata" format="rdata" from_work_dir="DiffBind_analysis.RData" label="${tool.name} on ${on_string}: RData file"> |
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169 <filter>out['rdata']</filter> |
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170 </data> |
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171 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript"> |
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172 <filter>out['rscript']</filter> |
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173 </data> |
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174 <data name="analysis_info" format="txt" from_work_dir="DiffBind_analysis_info.txt" label="${tool.name} on ${on_string}: Analysis info"> |
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175 <filter>out['analysis_info']</filter> |
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176 </data> |
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177 </outputs> |
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178 |
9
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179 <tests> |
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180 <!-- Ensure outputs work --> |
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181 <test expect_num_outputs="6"> |
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182 <repeat name="rep_group"> |
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183 <param name="groupName" value="Resistant"/> |
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184 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
11
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185 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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186 </repeat> |
11
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187 <repeat name="rep_group"> |
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188 <param name="groupName" value="Responsive"/> |
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189 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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190 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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191 </repeat> |
11
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192 <param name="scorecol" value="5" /> |
13
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193 <param name="format" value="interval"/> |
9
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194 <param name="pdf" value="True" /> |
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195 <param name="binding_matrix" value="True" /> |
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196 <param name="rdata" value="True" /> |
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197 <param name="rscript" value="True"/> |
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198 <param name="analysis_info" value="True"/> |
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199 <output name="outfile" ftype="interval" value="out_diffbind.interval" /> |
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200 <output name="plots" value="out_plots.pdf" compare="sim_size" /> |
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201 <output name="binding_matrix" value="out_binding_matrix.tab" /> |
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202 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/> |
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203 <output name="rscript"> |
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204 <assert_contents> |
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205 <has_text text="write.table"/> |
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206 </assert_contents> |
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207 </output> |
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208 <output name="analysis_info" compare="sim_size" > |
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209 <assert_contents> |
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210 <has_text text="SessionInfo"/> |
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211 </assert_contents> |
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212 </output> |
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213 </test> |
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214 <!-- Ensure control BAMs input works --> |
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215 <test expect_num_outputs="1"> |
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216 <repeat name="rep_group"> |
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217 <param name="groupName" value="Resistant"/> |
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218 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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219 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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220 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" /> |
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221 </repeat> |
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222 <repeat name="rep_group"> |
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223 <param name="groupName" value="Responsive"/> |
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224 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
c97a786e8fb5
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225 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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226 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" /> |
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227 </repeat> |
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228 <param name="scorecol" value="5" /> |
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229 <param name="format" value="interval"/> |
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230 <output name="outfile" ftype="interval" value="out_diffbind_ctrl.interval" /> |
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231 </test> |
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232 <!-- Ensure BED output works --> |
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233 <test expect_num_outputs="1"> |
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234 <repeat name="rep_group"> |
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235 <param name="groupName" value="Resistant"/> |
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236 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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237 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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238 </repeat> |
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239 <repeat name="rep_group"> |
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240 <param name="groupName" value="Responsive"/> |
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241 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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242 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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243 </repeat> |
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244 <param name="scorecol" value="5" /> |
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245 <param name="format" value="bed"/> |
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246 <output name="outfile" ftype="bed" value="out_diffbind.bed" /> |
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247 </test> |
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248 <!-- Ensure tabular output works --> |
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249 <test expect_num_outputs="1"> |
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250 <repeat name="rep_group"> |
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251 <param name="groupName" value="Resistant"/> |
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252 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
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253 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
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254 </repeat> |
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255 <repeat name="rep_group"> |
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256 <param name="groupName" value="Responsive"/> |
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257 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
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258 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
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259 </repeat> |
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260 <param name="scorecol" value="5" /> |
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261 <param name="format" value="tabular"/> |
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262 <output name="outfile" ftype="tabular" file="out_diffbind.tab" /> |
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263 </test> |
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264 </tests> |
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265 <help><![CDATA[ |
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266 |
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267 .. class:: infomark |
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268 |
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269 **What it does** |
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270 |
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271 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific |
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272 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and |
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273 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, |
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274 representing different ChIP experiments (antibodies, transcription factor and/or histone |
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275 marks, experimental conditions, replicates) as well as managing the results of multiple peak |
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276 callers. |
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277 |
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278 The primary emphasis of DiffBind is on identifying sites that are differentially bound |
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279 between two sample groups. It includes functions to support the processing of peak sets, |
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280 including overlapping and merging peak sets, counting sequencing reads overlapping intervals |
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281 in peak sets, and identifying statistically significantly differentially bound sites based on |
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282 evidence of binding affinity (measured by differences in read densities). To this end it uses |
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283 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages |
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284 edgeR and DESeq2). Additionally, the package builds on Rgraphics routines to provide a |
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285 set of standardized plots to aid in binding analysis. |
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286 |
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287 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of |
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288 examples: the first focusing on the core task of obtaining differentially bound sites based on |
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289 affinity data, the second working through the main plotting routines, the third discussing the |
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290 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail, |
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291 as well as comparing the results of an occupancy-based analysis with an affinity-based one. |
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292 Finally, certain technical aspects of the how these analyses are accomplished are detailed. |
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293 |
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294 **Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).** |
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295 |
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296 ----- |
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297 |
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298 **Inputs** |
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299 |
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300 DiffBind works primarily with peaksets, which are sets of genomic intervals representing |
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301 candidate protein binding sites. Each interval consists of a chromosome, a start and end |
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302 position, and usually a score of some type indicating confidence in, or strength of, the peak. |
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303 Associated with each peakset are metadata relating to the experiment from which the peakset |
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304 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to |
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305 be associated with each peakset (one for the ChIP data, and optionally another representing |
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306 a control sample) |
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307 |
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308 **Groups** |
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309 |
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310 You have to specify the name of the Group and the peak and BAM files for the two Groups you want to compare (e.g Resistant and Responsive) in the tool form above. |
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311 |
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312 Example: |
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313 |
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314 ============= ============= |
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315 **Sample** **Group** |
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316 ------------- ------------- |
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317 BT4741 Resistant |
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318 BT4742 Resistant |
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319 MCF71 Responsive |
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320 MCF72 Responsive |
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321 ============= ============= |
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322 |
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323 |
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324 **Peak files** |
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325 |
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326 Result of your Peak calling experiment in bed format, one file for each sample is required. The peak caller, format and score column can be specified in the tool form above. The default settings expect narrowPeak bed format, which has the score in the 8th column (-log10pvalue), and can be output from MACS2. |
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327 |
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328 Example: |
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329 |
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330 ======= ======= ======= =============== ============== |
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331 1 2 3 4 **5 (Score)** |
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332 ======= ======= ======= =============== ============== |
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333 chr18 215562 216063 peak_16037 56.11 |
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334 chr18 311530 312105 peak_16038 222.49 |
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335 chr18 356656 357315 peak_16039 92.06 |
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336 chr18 371110 372092 peak_16040 123.86 |
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337 chr18 395116 396464 peak_16041 1545.39 |
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338 chr18 399014 400382 peak_16042 1835.19 |
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339 chr18 499134 500200 peak_16043 748.32 |
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340 chr18 503518 504552 peak_16044 818.30 |
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341 chr18 531672 532274 peak_16045 159.30 |
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342 chr18 568326 569282 peak_16046 601.11 |
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343 ======= ======= ======= =============== ============== |
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344 |
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345 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required. |
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346 * Optional: Control BAM file representing a control dataset. If used, has to be specified for all samples. Note that the DiffBind authors say control reads are best utilized prior to running DiffBind, at the peak calling stage (e.g. with MACS2) and in blacklists, see this `Bioconductor post`_. |
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347 |
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348 ----- |
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349 |
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350 **Outputs** |
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351 |
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352 This tool outputs |
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353 |
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354 * a table of differentially bound sites in Interval, BED or Tabular 0-based format |
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355 |
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356 Optionally, under **Output Options** you can choose to output |
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357 |
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358 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots) |
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359 * a binding affinity matrix |
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360 * the R script used by this tool |
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361 * an RData file of the R objects generated |
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362 * a text file with information on the analysis (number of Intervals, FriP scores, method used) |
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363 |
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364 **Differentially Bound Sites** |
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365 |
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366 The default output is Interval format, for information on Interval format see here_. Alternatively, you can choose to output BED or Tabular 0-based format as below. For an explanation of the 0-based and 1-based coordinate systems see this `Biostars post`_. |
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367 |
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368 Example - **Interval format**: |
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369 |
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370 ====== ====== ====== ======== ===== ====== =========================================== |
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371 Chrom Start End Name Score Strand **Comment** |
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372 ====== ====== ====== ======== ===== ====== =========================================== |
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373 chr18 394599 396513 DiffBind 0 \. 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 |
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374 chr18 111566 112005 DiffBind 0 \. 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 |
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375 chr18 346463 347342 DiffBind 0 \. 879|5|5.77|3.24|2.52|6.51e-06|0.00303 |
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376 chr18 399013 400382 DiffBind 0 \. 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 |
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377 chr18 371109 372102 DiffBind 0 \. 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 |
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378 ====== ====== ====== ======== ===== ====== =========================================== |
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379 |
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380 Columns contain the following data: |
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381 |
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382 * **Chrom**: Chromosome name |
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383 * **Start**: Start position of site |
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384 * **End**: End position of site |
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385 * **Score**: 0 |
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386 * **Name**: DiffBind |
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387 * **Strand**: Strand |
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388 * **Comment**: The pipe ("|") separated values in this column correspond to: |
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389 |
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390 * *width*: Length of site |
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391 * *Conc*: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted) |
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392 * *Conc_Group1*: Mean concentration over the first group (e.g. Responsive) |
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393 * *Conc_Group2*: Mean concentration over second group (e.g. Resistant) |
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394 * *Fold*: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group. |
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395 * *p.value*: P-value confidence measure for identifying these sites as differentially bound |
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396 * *FDR*: a multiple testing corrected FDR p-value |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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397 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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398 Example - **BED format**: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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399 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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400 ===== ====== ====== ======== ===== ====== |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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401 Chrom Start End Name Score Strand |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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402 ===== ====== ====== ======== ===== ====== |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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403 chr18 394599 396513 DiffBind 0 \. |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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404 chr18 111566 112005 DiffBind 0 \. |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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405 chr18 346463 347342 DiffBind 0 \. |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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406 chr18 399013 400382 DiffBind 0 \. |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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407 chr18 371109 372102 DiffBind 0 \. |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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408 ===== ====== ====== ======== ===== ====== |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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409 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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410 Example - **Tabular format**: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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411 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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412 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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413 Chrom Start End Name Score Strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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414 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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415 chr18 394599 396513 DiffBind 0 \. 7.15 5.55 7.89 -2.35 7.06E-24 9.84E-21 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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416 chr18 111566 112005 DiffBind 0 \. 5.71 6.53 3.63 2.89 1.27E-08 8.88E-06 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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417 chr18 346463 347342 DiffBind 0 \. 5 5.77 3.24 2.52 6.51E-06 0.00303 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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418 chr18 399013 400382 DiffBind 0 \. 7.62 7 8.05 -1.04 1.04E-05 0.00364 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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419 chr18 371109 372102 DiffBind 0 \. 4.63 3.07 5.36 -2.3 8.10E-05 0.0226 |
1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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420 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== |
9
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421 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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422 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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423 **Binding Affinity Matrix** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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424 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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425 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent |
13
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426 differential analysis. Note that this output is a tabular 0-based format. |
9
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427 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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428 Example: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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429 |
12
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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430 ===== ====== ====== ========= ========= ========== ========== |
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1de83981d43c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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431 Chrom Start End MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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432 ===== ====== ====== ========= ========= ========== ========== |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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433 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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434 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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435 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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436 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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437 chr18 346464 347342 75.63583 40.96941 21.00995 16.80796 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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438 chr18 356560 357362 11.55547 14.70696 57.77737 53.57538 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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439 chr18 371110 372102 8.403982 9.454479 81.93882 82.98932 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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440 chr18 394600 396513 56.72687 43.07040 510.5419 438.0575 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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441 chr18 399014 400382 156.5241 117.6557 558.8648 496.8854 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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442 chr18 498906 500200 767.9138 278.3819 196.4430 181.7361 |
fa56d93f7980
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
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443 ===== ====== ====== ========= ========= ========== ========== |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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444 |
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445 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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446 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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447 **More Information** |
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448 |
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449 Generally, processing data with DiffBind involves five phases: |
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450 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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451 #. Reading in peaksets |
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452 #. Occupancy analysis |
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453 #. Counting reads |
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454 #. Differential binding affinity analysis |
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455 #. Plotting and reporting |
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456 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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457 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
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458 **Reading in peaksets**: |
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459 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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460 The first step is to read in a set of peaksets and associated |
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461 metadata. Peaksets are derived either from ChIP-Seq peak callers, such as **MACS2**, or using some other criterion (e.g. genomic windows, or all the promoter regions |
d7725c5596ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
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462 in a genome). A single experiment can have more than |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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463 one associated peakset; e.g. if multiple peak callers are used for comparison purposes |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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464 each sample would have more than one line in the sample sheet. Once the peaksets |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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465 are read in, a merging function finds all overlapping peaks and derives a single set of |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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466 unique genomic intervals covering all the supplied peaks (a consensus peakset for the |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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467 experiment). |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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468 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
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469 **Occupancy analysis**: |
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470 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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471 Peaksets, especially those generated by peak callers, provide |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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472 an insight into the potential occupancy of the protein being ChIPed for at specific |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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473 genomic loci. After the peaksets have been loaded, it can be useful to perform some |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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474 exploratory plotting to determine how these occupancy maps agree with each other, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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475 e.g. between experimental replicates (re-doing the ChIP under the same conditions), |
6171163112de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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476 between different peak callers on the same experiment, and within groups of samples |
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477 representing a common experimental condition. DiffBind provides functions to enable |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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478 overlaps to be examined, as well as functions to determine how well similar samples |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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479 cluster together. Beyond quality control, the product of an occupancy analysis may be |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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480 a consensus peakset, representing an overall set of candidate binding sites to be used |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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481 in further analysis. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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482 |
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483 **Counting reads**: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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484 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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485 Once a consensus peakset has been derived, DiffBind can use the |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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486 supplied sequence read files to count how many reads overlap each interval for each |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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487 unique sample. The peaks in the consensus peakset may be re-centered and trimmed |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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488 based on calculating their summits (point of greatest read overlap) in order to provide |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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489 more standardized peak intervals. The final result of counting is a binding affinity matrix |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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490 containing a (normalized) read count for each sample at every potential binding site. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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491 With this matrix, the samples can be re-clustered using affinity, rather than occupancy, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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492 data. The binding affinity matrix is used for QC plotting as well as for subsequent |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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493 differential analysis. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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494 |
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495 **Differential binding affinity analysis**: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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496 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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497 The core functionality of DiffBind is the |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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498 differential binding affinity analysis, which enables binding sites to be identified that |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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499 are statistically significantly differentially bound between sample groups. To accomplish |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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500 this, first a contrast (or contrasts) is established, dividing the samples into groups to |
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501 be compared. Next the core analysis routines are executed, by default using DESeq2. |
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502 This will assign a p-value and FDR to each candidate binding site indicating confidence |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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503 that they are differentially bound. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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504 |
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505 **Plotting and reporting**: |
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506 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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507 Once one or more contrasts have been run, DiffBind provides |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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508 a number of functions for reporting and plotting the results. MA plots give an |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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509 overview of the results of the analysis, while correlation heatmaps and PCA plots show |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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510 how the groups cluster based on differentially bound sites. Boxplots show the distribution |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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511 of reads within differentially bound sites corresponding to whether they gain or |
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512 lose affinity between the two sample groups. A reporting mechanism enables differentially |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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513 bound sites to be extracted for further processing, such as annotation, motif, and |
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514 pathway analyses. |
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515 |
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516 ----- |
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517 |
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518 **References** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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519 |
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520 DiffBind Authors: Rory Stark, Gordon Brown (2011) |
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521 Wrapper authors: Bjoern Gruening, Pavankumar Videm |
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522 |
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523 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
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524 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
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525 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf |
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526 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/ |
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527 .. _here: https://galaxyproject.org/learn/datatypes/#interval |
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528 .. _`Biostars post`: https://www.biostars.org/p/84686/ |
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529 |
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530 ]]> |
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531 </help> |
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532 <citations> |
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533 <citation type="doi">doi:10.1038/nature10730</citation> |
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534 </citations> |
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535 </tool> |