Question: counting the sequencing reads in 10kb regions on a genome-wide scale
gravatar for Bogdan
17 months ago by
Palo Alto, CA, USA
Bogdan850 wrote:

Dear all,

during a step of a CNV analysis on cancer genomes, I would like to be able to COUNT and DISPLAY along the CHROMOSOME AXIS the NUMBER of READS in 10KB REGIONS of GERMLINE and CANCER GENOMES.

I would like to ask you please for your suggestions about :

-- any fast function/algorithm that COUNTS the reads from a BAM file in 10kb windows ?

-- a package/function that DISPLAY the COUNTS along the chromosome axes ?

many thanks,


sequencing cnv genome • 570 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 17 months ago by Bogdan850

Thank you gentlemen.

Possibly, could I do it also in R, by using Rsamtools or a related package to COUNT the reads in specific genome WINDOWS ?

ADD REPLYlink written 17 months ago by Bogdan850

Yes, you could. But then you wouldn't match the speed:

In our tests, we can estimate depth across 60X genomes for 30 samples in 30 seconds.

ADD REPLYlink modified 17 months ago • written 17 months ago by h.mon26k
gravatar for igor
17 months ago by
United States
igor8.1k wrote:

You should be able to do it with bedtools. First generate a BED file of 10kb regions with bedtools makewindows. Then calculate coverage for those regions with bedtools coverage.

Alternatively, you can try deepTools bamCoverage to generate a coverage track (you can specify the size of bins).

Of course, whatever package you are using for CNV calling should have an option to generate some sort of graphical output.

ADD COMMENTlink modified 17 months ago • written 17 months ago by igor8.1k
gravatar for h.mon
17 months ago by
h.mon26k wrote:

Have a look at indexcov, but its intervals are of 16kb.

ADD COMMENTlink written 17 months ago by h.mon26k
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