Hello,
I am not sure if this has been answered before as I looked and couldn't find a simple answer.
I have a bam file, and all I want is to annotated all regions with 0 coverage in bed format. Is that possible?
Thank you,
Adrian
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written
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Adrian Pelin
You want the "genomecov" tool
Example:
$ bedtools genomecov -ibam aln.bam -bga | head
chr1 0 554304 0
chr1 554304 554309 5
chr1 554309 554313 6
chr1 554313 554314 1
chr1 554314 554315 0
chr1 554315 554316 6
chr1 554316 554317 5
chr1 554317 554318 1
chr1 554318 554319 2
chr1 554319 554321 6
To extract solely the intervals with no coverage just use awk to filter the results:
$ bedtools genomecov -ibam aln.bam -bga | awk '$4==0' | head -n 2
chr1 0 554304 0
chr1 554314 554315 0
Yup, definitely better than my answer (I misinterpreted 0 coverage to mean overlaps with a list of features). :P
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written
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Chris Fields
This is really cool! But then if I want to see what CDS features have a 0 coverage over the span of the the entire sequence of the CDS, how do I do that?
I could do bedtools intersect? I jsut need my CDS in .bed and then this output is also bed?
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written
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Adrian Pelin
This should work.
$ bedtools genomecov -ibam aln.bam -bga \
| awk '$4==0' \
| bedtools intersect -a cds.bed -b - -f 1.0
This has worked very well, thank you!
I am now looking to calculate average coverage for my CDS features, one value per CDS, and I can't seem to find any way to do that.
Hi, did you get an answer for this. I have tried using several bedtool subcommands but always get 0 coverage per cds. The same files show good coverge graphs in e.g. Geneous.
Hi Aaron,
I just want to bump one of the replies to this comment. I would also like to summarize coverage by region. Is that doable with bedtools?
This has worked very well, thank you!
I am now looking to calculate average coverage for my CDS features, one value per CDS, and I can't seem to find any way to do that.
Maybe have a look at bedtools and coverageBed. There are options to report depth at each position (if you want that resolution) and counts of overlaps for each.
-d Report the depth at each position in each B feature.
Positions reported are one based. Each position
and depth follow the complete B feature.
-counts Only report the count of overlaps, don't compute fraction, etc.
EDIT: forgot, but you would of course want to follow this by a filtering step (awk or grep) to get only the ones you want (e.g. the 0-count ones). Other alternatives would include running these through htseq-count or featureCounts followed by some similar filtering.
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written
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Chris Fields
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