[BioC] counting BAM reads in a set of genomic regions
Martin Morgan
mtmorgan at fhcrc.org
Fri Feb 8 15:05:39 CET 2013
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
>
> [[alternative HTML version deleted]]
>
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