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counting the sequencing reads in 10kb regions on a genome-wide scale

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,

bogdan

genome sequencing cnv
• 2,406 views • link
updated by Biostar Biostar • written by Bogdan Bogdan

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 ?

• 0 views • link
written by Bogdan Bogdan

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.

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written by h.mon h.mon

2 answers

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.

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written by igor igor

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

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written by h.mon h.mon

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