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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