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comparison bamCoverage.xml @ 43:c5787c91cab8 draft

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author bgruening
date Tue, 04 Feb 2014 09:02:21 -0500
parents 20f8dafb554f
children b9feca1f07f0
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42:ef1232cedacb 43:c5787c91cab8
1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.3"> 1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.4">
2 <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description> 2 <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <expand macro="stdio" /> 4 <expand macro="stdio" />
5 <macros> 5 <macros>
6 <token name="@BINARY@">bamCoverage</token> 6 <token name="@BINARY@">bamCoverage</token>
29 #end if 29 #end if
30 #elif $scaling.type=='own': 30 #elif $scaling.type=='own':
31 --scaleFactor $scaling.scaleFactor 31 --scaleFactor $scaling.scaleFactor
32 #end if 32 #end if
33 33
34 #if str(region).strip() != '': 34 #if str($region).strip() != '':
35 --region 'region' 35 --region '$region'
36 #end if 36 #end if
37 37
38 #if $advancedOpt.showAdvancedOpt == "yes": 38 #if $advancedOpt.showAdvancedOpt == "yes":
39 #if $advancedOpt.smoothLength: 39 #if $advancedOpt.smoothLength:
40 --smoothLength '$advancedOpt.smoothLength' 40 --smoothLength '$advancedOpt.smoothLength'
131 </outputs> 131 </outputs>
132 <help> 132 <help>
133 133
134 **What it does** 134 **What it does**
135 135
136 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or read coverages. 136 Given a BAM file, this tool generates a bigWig or bedGraph file with genome-wide coverage of fragment or read coverages.
137 The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not) 137 The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not)
138 that overlap each bin in the genome. Bins with zero counts are skipped, i.e. not added to the output file. 138 that overlap each bin (a region of fixed length, i.e. 25 bp) in the genome. Bins with zero counts are skipped, i.e. not added to the output file.
139 The resulting read counts can be normalized using either a given scaling factor, the RPKM formula or to get a 1x depth of coverage (RPGC). 139 The resulting read counts can be normalized using either a given scaling factor, the RPKM formula or to get a 1x depth of coverage (RPGC).
140 140
141 141
142 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png 142 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
143 143
144 144
145 You can find more details in the `bamCoverage wiki`_. 145 You can find more details on the bamCoverage wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
146
147 .. _bamCoverage wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
148 146
149 147
150 **Output files**: 148 **Output files**:
151 149
152 - coverage file either in bigWig or bedGraph format 150 - coverage file either in bigWig or bedGraph format