What version of bedtools? You need to use the -split option
c.f. http://code.google.com/p/bedtools/wiki/History Version 2.8.0 (July-05-2010) Proper support for "split" BAM alignments and "blocked" BED (aka BED12) features. By using the "-split" option, intersectBed, coverageBed, genomeCoverageBed, and bamToBed will now correctly compute overlaps/coverage solely for the "split" portions of BAM alignments or the "blocks" of BED12 features such as genes. Cheers, Malcolm Cook > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Carlos > Javier Borroto > Sent: Thursday, February 24, 2011 10:46 AM > To: [email protected] > Subject: [Genome] Problem with BAM coverage support through > BEBTools / genomeCoverageBed > > Hi, > > After reading: > https://lists.soe.ucsc.edu/pipermail/genome/2010-September/023404.html > > And wanting to display coverage for a BAM track in a local > mirror, I went ahead and use the approach described by Assaf > Gordon, thanks a lot, the pdf file was very helpful. But I'm > having a problem, my data comes from RNA-seq and the coverage > track I get after: > > $ genomeCoverageBed -bg -ibam [SAMPLE.SORTED.BAM] \ -g > [CHROM_SIZE] > [SAMPLE.BEDGRAPH] $ bedGraphToBigWig > [SAMPLE.BEDGRAPH] [CHROM_SIZE] [SAMPLE.BW] > > With a trackDB.ra file like this: > > track bamCoverage > compositeTrack on > shortLabel BAM coverage > longLabel Coverage of BAM files > group local > priority 4.1 > visibility hide > type bigWig > > track bamCoverage1 > parent bamCoverage on > shortLabel BAM Coverage 1 > longLabel BAM 1 reads coverage > > Although displaying, is showing a graph with coverage for the > gap area where reads expand through splice junctions, I would > like this not to occur, I would like for this area to show 0 > coverage as it masks the actual coverage of my data. > > Any help including other approaches to get coverage > information for a BAM track will be highly appreciated. > Thanks, > -- > Carlos Javier Borroto > Baltimore, MD > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
