[Bioc-sig-seq] Rsamtools

Dykema, Karl Karl.Dykema at vai.org
Wed Jan 27 23:00:53 CET 2010

Hi all,

We have been using Rsamtools to import BAM files also. On previous sequencing runs the BAM files were around 800 megs and I could import the entire BAM with .readAligned_bam(). Our new sequencing data creates larger BAM files and I am unable to import them like before. So, as Steve pointed out to me offline, I probably will need to import the reads from each chromosome individually. Unfortunately it does not seem to be recognizing my chromosome names, error msg below. Has anyone had a similar problem or recognize something that I might be doing incorrectly? Thanks in advance.

> which <- RangesList(chr1=IRanges(start=1,end=247249719))
> params <- ScanBamParam(which=which)
> chr1reads <- scanBam("../aln.sorted.nodupes.bam",param=params)
Error in function (bam, tmpl, space, start, end)  : failed to scan BAM
  file: �
  last record: 0
In addition: Warning message:
In function (bam, tmpl, space, start, end)  : 'space' not in BAM header
  file: ../aln.sorted.nodupes.bam
  space: chr1

Karl Dykema
Computational Biologist
Van Andel Research Institute

-----Original Message-----
From: bioc-sig-sequencing-bounces at r-project.org [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of Steve Lianoglou
Sent: Tuesday, January 26, 2010 9:59 AM
To: Aurelie Laugraud
Cc: Bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] Rsamtools


On Tue, Jan 26, 2010 at 9:41 AM, Aurelie Laugraud <laugraud at prabi.fr> wrote:
> Dear all,
> I have read about Rsamtools being in dev repositories and advices about waiting for it to be stable to use it ...
> my question is therefore how long before it comes as a "regular"  R package ? Or is that that awful to make the dev version working ?
> I am using mac os X 10.6.2

For what it's worth, I'm using the version of Rsamtools from SVN in
order to read BAM files, and it works "as advertised". Note that this
means you (should be) using R 2.11 (you can get it from here:


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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