[BioC] Reading paired-end data into GRangesList

[Cory Barr]

Hi Hubert,

Try the grglist function on a GappedAlignments object.

gapped_alignments <- readBamGappedAlignments(bam_file)
granges_list <- grglist(gapped_alignments)

Then to combine each end of the read from the different ends into the
same element of the GRangesList, try the "split" function on the names
of the reads.

-Cory

On Wed, Oct 26, 2011 at 6:51 AM, Hubert Rehrauer
<Hubert.Rehrauer at fgcz.ethz.ch> wrote:
> Hi
>
> I want to load paired-end data from Bam-Files into R in order to do
> expression counting. The complicating thing is, that the first read was
> aligned using a gapped alignment (i.e. the cigar string contains Ns).
>
> How can this be done? I thought this would be a quite common task but I did
> not find any function that would do this. Neither scanBam nor
> readBamGappedAlignments are directly helpful with this.
>
> For me the most obvious thing would be to hold the alignment of such a read
> as a GRangesList. In order to get there I would use scanBam to load the
> first read. Parse the  cigar string to identify the gaps, build a
> GRangesList and then add the alignment of the second read to the List. Do
> you have any better ideas?
>
>
> best regards,
> hubert
>
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