[BioC] counting BAM reads in a set of genomic regions

[Martin Morgan]

On 02/08/2013 05:49 AM, mattia pelizzola wrote:
> Hi everybody,
> given a BAM file and a set of genomic regions stored in a GRanges object,
> I would like to know your opinion/experience on the fastest (and memory
> parsimonious) way in BioC for counting the number of reads for each region.

Rsamtools::countBam is memory efficient and reasonably fast.

   which = <my GRanges>
   param = ScanBamParam(which=which)
   countBam(<my BAM file, param=param)

For several files

   countBam(BamFileList(<my BAM filess>), param=param)

See also ?summarizeOverlaps in the GenomicRanges pacakge.

Martin

>
> Thanks!
>
> mattia
>
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