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