On 06/02/2011 01:45 AM, David A. wrote:
Dear Martin, thanks a lot for your suggestion, but I am getting an error
with one of the samples. The other sample seems to load fine, so it
could be that this one is too large. I haven't found information about
this error, can you suggest something?
> pars<-ScanBamParam(flag=scanBamFlag(isProperPair=TRUE),
what=c("rname","strand","pos","qwidth","seq","isize"))
> data7<-scanBam('/Data/run5/aligned/s_7.bam',param=pars)[[1]]
Error in .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param
= param) :
too many nucleotides, use 'param=ScanBamParam(which=<...>)'
Hi Dave -- this is an issue with Rsamtools that is on my radar to
address. The problem is with the 'seq' argument, where the total number
of nucleotides exceeds the maximum integer R can represent (2^31 - 1).
The workaround is either to omit 'seq' or to read the data in chunks
(e.g., by chromosome, which="chr1") and concatenate (c(chr1rd, chr2rd);
probably you'd do listOfRangedData = lapply(chrs, function(chr, ...) {
<input chr to RangedData> }); rd = do.call(c, listOfRangedData).
Martin
It is prompting for using 'which' argument, I guess to select a part of
the file (alignment against hg19), but how can I deal with the BAM file
if I want to load it complete and then calculate the overall mean insert
size?
Thanks,
Dave
> Date: Tue, 31 May 2011 17:12:22 -0700
> From: mtmor...@fhcrc.org
> To: dasol...@hotmail.com
> CC: bioc-sig-sequencing@r-project.org
> Subject: Re: [Bioc-sig-seq] transforming bam for TEQC
>
> 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]]
> >
> > _______________________________________________ Bioc-sig-sequencing
> > mailing list Bioc-sig-sequencing@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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