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Question: counting BAM reads in a set of genomic regions
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gravatar for mattia pelizzola
4.8 years ago by
mattia pelizzola200 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. Thanks! mattia [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.8 years ago by Martin Morgan ♦♦ 20k • written 4.8 years ago by mattia pelizzola200
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gravatar for Martin Morgan
4.8 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 4.8 years ago by Martin Morgan ♦♦ 20k
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