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
