counting BAM reads in a set of genomic regions
1
0
Entering edit mode
@mattia-pelizzola-3304
Last seen 5 months ago
Italy
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]]
• 934 views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 6 weeks ago
United States
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 COMMENT

Login before adding your answer.

Traffic: 883 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6