On 05/31/2011 05:42 AM, David A. wrote:
Hi, I would like to load my paired-end bam file for TEQC using the
TEQC library. In the manual it says that the bed file needed for
paired-end reads should contain read pair ID. How can I get this
format? Some bam2bed converters I know only give the three main
columns, and if I am not wrong the BEDPE format is too ample.
Hi Dave -- I haven't used TEQC (looks good, though) but since its
get.reads function returns a RangedData object with mate pairs as
successive rows (from example(get.reads); reads) it seems like this
could be constructed directly from your bam file using
Rsamtools::scanBam and IRanges::RangedData. I think you'll start with
something like
param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE),
what=c("qname", "pos", "qwidth", "rname"))
aln = scanBam(fl, param=param)[[1]]
rd = with(aln, RangedData(IRanges(pos, width=qwidth), ID=qname,
space=rname))
rd[order(rd$space, rd$ID)]
Martin
Any help would be greatly appreciated
Cheers,
Dave [[alternative HTML version deleted]]
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