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

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