[Bioc-sig-seq] transforming bam for TEQC

Martin Morgan mtmorgan at fhcrc.org
Wed Jun 1 02:12:22 CEST 2011

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,

   rd[order(rd$space, rd$ID)]


> Any help would be greatly appreciated
> Cheers,
> Dave  [[alternative HTML version deleted]]
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