I have sequenced a cell line exposed to UV and would like to know if any genes have been deleted compared to the ancestor. I extracted the CDS regions from the annotation file to annotation.bed and ran coverageBed in order to find the read depth at any given exon
coverageBed -abam DXB11.bam -b annotation.bed > depth.txt
the output for a particular domain was
NW_003614442.1 464809 465646 158 837 837 1.0000000
So 100% of the region 464809-465646 had a depth of 158 and that entire region of 837 bp was that depth, correct?
That that is very high as the theoretical depth should be 35. So i looked into the depth at every position of the genome
/BEDTools-Version-2.16.2/genomeCoverageBed -d -ibam DXB11.bam > DXB11.coverage
and looked into the same region (464809-465646) and done this way it had a median depth of 18 = much more realistic.
Are you able to see what i did wrong or maybe advice me another way of more easily getting to a median depth of each exon in the genome from a bam file?
coverageBed -abam DXB11.bam -b annotation.bed > depth.txt
the output for a particular domain was
NW_003614442.1 464809 465646 158 837 837 1.0000000
So 100% of the region 464809-465646 had a depth of 158 and that entire region of 837 bp was that depth, correct?
That that is very high as the theoretical depth should be 35. So i looked into the depth at every position of the genome
/BEDTools-Version-2.16.2/genomeCoverageBed -d -ibam DXB11.bam > DXB11.coverage
and looked into the same region (464809-465646) and done this way it had a median depth of 18 = much more realistic.
Are you able to see what i did wrong or maybe advice me another way of more easily getting to a median depth of each exon in the genome from a bam file?
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