counting the sequencing reads in 10kb regions on a genome-wide scale
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Bogdan ▴ 620
@bogdan-2367
Last seen 7 days ago
Palo Alto, CA, USA

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 in R that COUNTS the reads from a BAM file in 10kb windows ? (possibly with Rsamtools ... )

-- a package/function that DISPLAY the COUNTS along the chromosomes ?

many thanks,

bogdan

read counting CNV rsamtools • 392 views
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@james-w-macdonald-5106
Last seen 16 minutes ago
United States

That's pretty much exactly what csaw does so you might look at that package.

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Thank you James !

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