[Bioc-devel] accessing gapped alignment
mtmorgan at fhcrc.org
Mon Dec 20 14:34:01 CET 2010
On 12/20/2010 05:27 AM, Daniel.Berner at unibas.ch wrote:
> dear developers
> I have performed a gapped alignment of my illumina reads. I now want to
> analyze the output by accessing the CHROMOSOME and POSITION information
> contained in the BAM file. I therefore uploaded the BAM using
> readAligned(), but found that
> all those reads aligning to the reference genome with a GAP are missing.
> However, when using readGappedAlignments(), I loose information crucial
> to my analysis (i.e., chromosome, position). Is there any way to upload
> into R GAPPED
> alignments while preserving read ID, chromosome, position etc?
Rsamtools::scanBam lets you read whatever you want, returning a list
with the corresponding data.
What is that you want to do with the data once in R?
> Daniel Berner
> Bioc-devel at r-project.org mailing list
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Telephone: 206 667-2793
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