Question: counting the sequencing reads in 10kb regions on a genome-wide scale
0
gravatar for Bogdan
21 months ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 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

rsamtools cnv read counting • 297 views
ADD COMMENTlink modified 21 months ago by James W. MacDonald52k • written 21 months ago by Bogdan580
Answer: counting the sequencing reads in 10kb regions on a genome-wide scale
3
gravatar for James W. MacDonald
21 months ago by
United States
James W. MacDonald52k wrote:

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

ADD COMMENTlink written 21 months ago by James W. MacDonald52k

Thank you James !

ADD REPLYlink written 21 months ago by Bogdan580
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 227 users visited in the last hour