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comparison bamCoverage.xml @ 45:b9feca1f07f0 draft

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author bgruening
date Mon, 31 Mar 2014 17:48:50 -0400
parents c5787c91cab8
children 72d1d7c68bd3
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44:3fc7efe86cfc 45:b9feca1f07f0
1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.4"> 1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
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>
58 <param name="bamInput" format="bam" type="data" label="BAM file" 58 <param name="bamInput" format="bam" type="data" label="BAM file"
59 help="The BAM file must be sorted."/> 59 help="The BAM file must be sorted."/>
60 60
61 <param name="fragmentLength" type="integer" value="300" min="1" 61 <param name="fragmentLength" type="integer" value="300" min="1"
62 label="Length of the average fragment size" 62 label="Length of the average fragment size"
63 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."/> 63 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;). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
64 64
65 <param name="binSize" type="integer" value="50" min="1" 65 <param name="binSize" type="integer" value="50" min="1"
66 label="Bin size in bp" 66 label="Bin size in bp"
67 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/> 67 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
68 68
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 with genome-wide coverage of fragment or read coverages. 136 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
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 read coverages. The way the method works is by first calculating all the
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. 138 number of reads (either extended to match the fragment length or not) that
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 overlap each bin in the genome. The resulting read counts can be normalized
140 140 using either a given scaling factor, the RPKM formula or to get a 1x depth of
141 coverage (RPGC). In the case of paired-end mapping each read mate is treated
142 independently to avoid a bias when a mixture of concordant and discordant
143 pairs is present. This means that *each end* will be extended to match the
144 fragment length.
141 145
142 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png 146 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
143 147
144 148
145 You can find more details on the bamCoverage wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage 149 You can find more details on the bamCoverage wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage