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comparison bamCompare.xml @ 24:d7c9fd76e41e draft

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author bgruening
date Tue, 04 Feb 2014 09:12:07 -0500
parents 8c452f37c896
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23:8c452f37c896 24:d7c9fd76e41e
72 #end if 72 #end if
73 73
74 </command> 74 </command>
75 75
76 <inputs> 76 <inputs>
77 <param name="bamFile1" format="bam" type="data" label="Treatment BAM file" 77 <param name="bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"
78 help="The BAM file must be sorted."/> 78 help="The BAM file must be sorted."/>
79 79
80 <param name="bamFile2" format="bam" type="data" label="BAM file" 80 <param name="bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"
81 help="The BAM file must be sorted."/> 81 help="The BAM file must be sorted."/>
82 82
83 <param name="fragmentLength" type="integer" value="300" min="1" 83 <param name="fragmentLength" type="integer" value="300" min="1"
84 label="Length of the average fragment size" 84 label="Length of the average fragment size"
85 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> 85 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
90 90
91 <conditional name="scaling"> 91 <conditional name="scaling">
92 <param name="method" type="select" 92 <param name="method" type="select"
93 label="Method to use for scaling the largest sample to the smallest"> 93 label="Method to use for scaling the largest sample to the smallest">
94 <option value="readCount" selected="true">read count</option> 94 <option value="readCount" selected="true">read count</option>
95 <option value="SES">signal extraction scaling (SES)</option> 95 <option value="SES">signal extraction scaling (SES), check the bamFingerprint plot before using it!</option>
96 <option value="own">enter own scaling factors</option> 96 <option value="own">enter own scaling factors</option>
97 </param> 97 </param>
98 <when value="SES"> 98 <when value="SES">
99 <param name="sampleLength" type="integer" value="1000" min="10" 99 <param name="sampleLength" type="integer" value="1000" min="10"
100 label="Length in base pairs used to sample the genome and compute the size or scaling factors to compare the two BAM files " 100 label="Length in base pairs used to sample the genome and compute the size or scaling factors to compare the two BAM files "
203 203
204 204
205 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png 205 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
206 206
207 207
208 You can find more details in the `bamCompare wiki`_. 208 You can find more details on the bamCompare wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
209
210 .. _bamCompare wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
211 209
212 210
213 **Output files**: 211 **Output files**:
214 212
215 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files. 213 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.