diff bamCoverage.xml @ 45:b9feca1f07f0 draft

Uploaded

--- a/bamCoverage.xml	Tue Feb 04 09:11:10 2014 -0500
+++ b/bamCoverage.xml	Mon Mar 31 17:48:50 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.4">
+<tool id="deeptools_bamCoverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
     <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -60,7 +60,7 @@
 
         <param name="fragmentLength" type="integer" value="300" min="1"
             label="Length of the average fragment size"
-            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."/>
+            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."/>
 
         <param name="binSize" type="integer" value="50" min="1" 
             label="Bin size in bp"
@@ -133,11 +133,15 @@
 
 **What it does**
 
-Given a BAM file, this tool generates a bigWig or bedGraph file with genome-wide coverage of fragment or read coverages. 
-The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not) 
-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. 
-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).
-
+Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
+read coverages. The way the method works is by first calculating all the
+number of reads (either extended to match the fragment length or not) that
+overlap each bin in the genome. 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). In the case of paired-end mapping each read mate is treated
+independently to avoid a bias when a mixture of concordant and discordant
+pairs is present. This means that *each end* will be extended to match the
+fragment length.
 
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png