Question: counting the sequencing reads in 10kb regions on a genome-wide scale
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Bogdan • 580 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 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
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modified 21 months ago
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James W. MacDonald ♦ 52k
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written
21 months ago by
Bogdan • 580

