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comparison bamCoverage.xml @ 28:f7712a057440 draft

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new bugfix release
author bgruening
date Wed, 02 Apr 2014 09:15:44 -0400
parents bf1b1dcdd67b
children 3a2aab18a217
comparison
equal deleted inserted replaced
27:bf1b1dcdd67b 28:f7712a057440
1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.5"> 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>
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