I am trying to use genomeCoverageBed in the bedTools suite to find coverage of each base in the human genome from an RNA seq bam file that has been generated with TopHat. The output file gets enormous because all of the positions with 0 hits are included. Is there a way I can get the output file to include only chromosome-coordinate pairs that have non-zero hits? This is the command that I use to generate the output file:
genomeCoverageBed -ibam bamfile.bam -g human.hg19.genome -d -split > genome_coverage_split_071711_1.txt
Thanks.
Eric
genomeCoverageBed -ibam bamfile.bam -g human.hg19.genome -d -split > genome_coverage_split_071711_1.txt
Thanks.
Eric
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