Good Morning Carlos: Here is an alternative procedure to create a coverage graph for a bam file:
https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024318.html For assistance with BEDTools, please consult the bedTools project: http://code.google.com/p/bedtools/ Can you intersect your graph with 'NOT gap' in the table browser to display the graph in areas that are not gap ? --Hiram Carlos Javier Borroto wrote: > 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
