Question: Genome coverage within specified regions
0
gravatar for ilovesuperheroes1993
7 weeks ago by
ilovesuperheroes19930 wrote:

Hi, I have a bed file containing the coordinates of certain regions of the genome. I want to get the genome coverage of these regions at each base position (i,e, similar to using -d option in bedtools genomecov).

example bed file

chr1 100 200 chr5 250 300

I want the output in the following manner:

chr1 100 "coverage at this position" chr1 101 "coverage" chr1 102 "coverage" . . . chr1 199 "coverage" chr1 200 "coverage" chr5 250 "coverage" chr5 251 "coverage" ...and so on

The genomecov of bedtools does this for the entire genome. Is there any way to get the coverage within the regions specified only?

coverage genomecov bedtools • 102 views
ADD COMMENTlink modified 7 weeks ago by ATpoint23k • written 7 weeks ago by ilovesuperheroes19930

https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html

bedtools coverage [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>
ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by 2nelly170
1
gravatar for ATpoint
7 weeks ago by
ATpoint23k
Germany
ATpoint23k wrote:

Mosdepth for the win (https://github.com/brentp/mosdepth ):

-b --by <bed|window> optional BED file or (integer) window-sizes.

ADD COMMENTlink modified 7 weeks ago by lieven.sterck5.9k • written 7 weeks ago by ATpoint23k
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