[Bioc-devel] accessing gapped alignment

[Martin Morgan]

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.

  library(Rsamtools)
  example(scanBam)

What is that you want to do with the data once in R?

Martin


> thanks,
> Daniel Berner
> 
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