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annotate slamdunk.xml @ 1:57bf9a0d49a5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
author iuc
date Sun, 20 Jan 2019 06:51:15 -0500
parents 3fd7458bc861
children fae4a5ec0653
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1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy1">
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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3 <macros>
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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4 <import>macros.xml</import>
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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5 </macros>
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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6 <expand macro="requirements" />
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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7 <version_command>slamdunk --version</version_command>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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8 <command detect_errors="exit_code"><![CDATA[
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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9 #if $reference_source.reference_source_selector == 'history':
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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10 ln -f -s '$reference_source.ref_file' reference.fa &&
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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11 #else:
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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12 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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13 #end if
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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14 slamdunk all -r reference.fa -b '$Reference' -o ./out
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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15 -n $multimapper.multimappers
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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16 $multimapper.multimap
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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17 #if $multimapper.filterbed.bedtofilter:
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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18 -fb $multimapper.filterbed.bedtofilter
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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19 #end if
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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20 -5 $quantseq.trim5
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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21 -a $quantseq.maxpolyA
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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22 $advanced.endtoend
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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23 -mq $advanced.minMQ
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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24 -mi $advanced.minID
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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25 -nm=$advanced.maxNM
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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26 -mc $advanced.minCov
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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27 -mv $advanced.minVar
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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28 -mbq $advanced.minBaseQual
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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29 -rl $readLength
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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30 -c $covThresh
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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31 '$Reads'
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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32 ]]></command>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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33 <inputs>
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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34 <expand macro="reference_files" />
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
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35 <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ files"/>
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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36 <section name="multimapper" title="Multimapper recovery"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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37 expanded="false">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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38 <section name="filterbed"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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39 title="Use separate 3' UTR bed to filter multimappers." expanded="false">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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40 <param name="bedtofilter" type="data" format="bed" optional="true"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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41 label="Bed to filter" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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42 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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43 <param name="multimappers" type="integer" min="1" value="1"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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44 label="Maximum number of alignments to report per read"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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45 help="The maximum number of alignments is used to track multimapping read alignments. The more are allowed, the more sensitive the multimapper filtering will be, but also the longer the runtime will be. 100 was used in previous publications." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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46 <param name="multimap" type="boolean" truevalue="--multimap" falsevalue=""
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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47 label="Use reference bed file to resolve multimappers."
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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48 help="Enable multimapper recovery, requires -n to be set to a value > 1 to have impact." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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49 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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50 <section name="quantseq" title="Quantseq" expanded="false">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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51 <param name="trim5" type="integer" min="0" value="12"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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52 label="Number of bp to remove from the 5' end of all reads"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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53 help="For Lexogen's Quantseq kit and previous SLAM-seq papers a clipping of 12 bp from the 5' end is recommended." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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54 <param name="maxpolyA" type="integer" min="0" value="4"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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55 label="Maximum number of As at the 3' end of a read"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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56 help="The maximum number of allowed As at the 3' end of a read. All A-stretches that exceed this threshold are clipped because they are likely part of the poly-A tail." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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57 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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58 <section name="advanced" title="Advanced settings." expanded="false">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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59 <param name="endtoend" type="boolean" truevalue="--endtoend" falsevalue=""
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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60 label="Enable end-to-end alignments for mapping."
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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61 help="Enable end-to-end alignments for mapping in slamdunk with --endtoend" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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62 <param name="minMQ" type="integer" min="0" value="2"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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63 label="Minimum mapping quality"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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64 help="Minimum mapping quality to consider alignments (default: 2)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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65 <param name="minID" type="float" min="0" value="0.95"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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66 label="Minimum alignment identity"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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67 help="Minimum alignment-identity to consider alignments (default: 0.95)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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68 <param name="maxNM" type="integer" value="-1"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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69 label="Maximum number of mismatches"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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70 help="Maximum number of mismatches to consider alignments. Negative numbers deactivate filter (default: -1)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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71 <param name="minCov" type="integer" min="0" value="10"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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72 label="Minimum coverage to call variant"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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73 help="Minimum coverage to call variant (default: 10)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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74 <param name="minVar" type="float" min="0" value="0.8"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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75 label="Minimum variant fraction to call variant"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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76 help="Minimum variant fraction to call variant (default: 0.8)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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77 <param name="minBaseQual" type="integer" min="0" value="27"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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78 label="Minimum base quality"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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79 help="Minimum base quality for T>C conversions (default: 27)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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80 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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81 <param name="covThresh" type="integer" min="1" value="1"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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82 label="T>C conversion threshold"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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83 help="Number of T>C conversions required to count a read as a T>C read (default: 1)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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84 <param name="readLength" type="integer" min="50" value="50"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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85 label="Read length"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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86 help="Maximum read length (before trimming)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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87 </inputs>
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88 <outputs>
1
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89 <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" label="${tool.name} on ${on_string}: BAM"/>
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90 <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" label="${tool.name} on ${on_string}: Count TSV"/>
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91 <data name="outputVcf" format="vcf" from_work_dir="./out/snp/*vcf" label="${tool.name} on ${on_string}: VCF"/>
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92 </outputs>
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93 <tests>
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94 <test>
1
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95 <!--Ensure default outputs work -->
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96 <param name="reference_source_selector" value="history" />
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97 <param name="ref_file" value="ref.fa" />
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98 <param name="Reference" value="actb.bed" />
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99 <param name="Reads" value="reads.fq" />
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100 <param name="readLength" value="100" />
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101 <section name="quantseq">
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102 <param name="trim5" value="0" />
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103 </section>
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104 <section name="advanced">
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105 <param name="minBaseQual" value="27" />
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106 </section>
1
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107 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
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108 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
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109 lines_diff="2" />
1
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110 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
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111 </test>
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112 <test>
1
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113 <!--Ensure built-in fasta works -->
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114 <param name="reference_source_selector" value="cached" />
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115 <param name="Reference" value="actb.bed" />
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116 <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
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117 <param name="readLength" value="100" />
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118 <section name="quantseq">
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119 <param name="trim5" value="0" />
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120 </section>
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121 <section name="advanced">
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122 <param name="minBaseQual" value="27" />
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123 </section>
1
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124 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
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125 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
0
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126 lines_diff="2" />
1
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127 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
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128 </test>
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129 </tests>
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130 <help><![CDATA[
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131 SLAM-seq
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132 ========
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133
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134 SLAM-seq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability.
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135
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136 Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 <https://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4435.html>`_
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137
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138 Slamdunk
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139 ========
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140
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141 To analyze a given SLAM-seq dataset with *slamdunk* without recovering multimappers, you only need to provide the following files and keep everything else to the default parameters.
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142
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143 =============== ==========================================================================================================================================================
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144 Parameter Description
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145 =============== ==========================================================================================================================================================
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146 **Genome** The reference fasta file (Genome assembly).
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147 **Reference** BED-file containing coordinates for 3' UTRs.
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148 **Reads** Sample FASTQ(gz) files.
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149 **Read length** Maximum length of reads (usually 50, 100, 150).
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150 =============== ==========================================================================================================================================================
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151
1
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152 This will run the entire *slamdunk* analysis (`slamdunk all`) with the most relevant output files being:
0
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153
1
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154 * Tab-separated *tcount* file (Count TSV) containing the SLAM-seq statistics per UTR
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155 * BAM-file with the final filtered mapped reads
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156 * VCF file of variants called on the final filtered alignments
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157
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158 These files can be input to the **Alleyoop** tool for visualization and further processing. See the `Slamdunk documentation`_ for more information.
0
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159
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160 ------------------------------------------------------
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161
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162 Multimapper recovery
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163 --------------------
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164
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165 To utilize multimapper recovery, modify the following parameters. You must either choose a separate 3' UTR file or activate filtering
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166 on the supplied reference file. Will only yield different results than a unique-mapping run by specifying a number > 1 as maximum number of multimapper aligments to consider.
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167
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168 =================================================== =========================================================
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169 Parameter Description
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170 =================================================== =========================================================
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171 **Maximum number of alignments to report per read** The maximum number of multimapper alignments to consider.
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172 **Use separate 3' UTR bed to filter multimappers.** 3' UTR bed file to filter.
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173 **Use reference bed file to resolve multimappers.** Use reference as 3' UTR bed file to filter.
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174 =================================================== =========================================================
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175
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176 ------------------------------------------------------
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178 T>C conversions
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179 ---------------
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181 Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; http://doi.org/10.1126/science.aao2793 <http://science.sciencemag.org/content/early/2018/04/04/science.aao2793>`_
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183 This can be controlled by the following parameter:
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185 ============================ ================================================================================
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186 Parameter Description
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188 **T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read.
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189 ============================ ================================================================================
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190
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191 .. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html
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193 ]]></help>
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194 <citations>
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195 <expand macro="citations" />
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196 </citations>
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197 </tool>