Hello everyone,
So I just want to compute the average coverage per base for our exome-seq. First I collected all the exons in a bed file, say exon.bed and it looks like this:
chr1 11873 12227
chr1 12594 12721
I also have an exam seq bam file, and what I did is:
samtools view -b bamfile.bam | coverageBed -abam stdin -b exon.bed -d > report, which looks like this:
chr1 161480623 161480746 1 0
chr1 161480623 161480746 2 0
chr1 161480623 161480746 3 0
chr1 161480623 161480746 4 0
chr1 161480623 161480746 5 0
chr1 161480623 161480746 6 0
But the thing is the last column is always zero. What did I do wrong? Thank you guys for your help!
So I just want to compute the average coverage per base for our exome-seq. First I collected all the exons in a bed file, say exon.bed and it looks like this:
chr1 11873 12227
chr1 12594 12721
I also have an exam seq bam file, and what I did is:
samtools view -b bamfile.bam | coverageBed -abam stdin -b exon.bed -d > report, which looks like this:
chr1 161480623 161480746 1 0
chr1 161480623 161480746 2 0
chr1 161480623 161480746 3 0
chr1 161480623 161480746 4 0
chr1 161480623 161480746 5 0
chr1 161480623 161480746 6 0
But the thing is the last column is always zero. What did I do wrong? Thank you guys for your help!
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