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Old 09-19-2013, 11:25 AM   #1
Location: Seattle

Join Date: Jul 2011
Posts: 98
Default bedtools coverage is inaccurate

I am using bedtools to calculate coverage in an RNA-seq bam file. I get screwy readings when it encounters a gap where there are no reads. Rather than filling it in with zeros, it takes a value that is somewhere near the last read and uses that value to fill across the gap. For example, I just looked in IGV at a suspicious area in a bam file. IGV shows readcounts of 11, 11, 10, 10, 10, 9, 9, 9, 9, 1 and then a bunch of zeros. bedtools, on the other hand, lists the same numbers except that when it comes to the final 1, it says 7, and then the very long list of zeros is instead a very long list of 7s. Can anyone suggest a solution? The code I used is pasted below. (The last little thing where I pipe results to grep is to output only lines with non-zero read counts. Perhaps that's where I'm screwing up, but I don't think so.)



genomeCoverageBed -d -split -ibam input.bam -g /home/efoss/gene_databases/dot_genome_files/g1k_v37.genome | grep -v -P "\S+\t\S+\t0" > output.txt

Last edited by efoss; 09-19-2013 at 11:48 AM.
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