Hi Sean,

Thanks for the hint. In my case, the pileup functions do not help much, as
I'm interested in finding the mismatches per read/alignment, whereas the
pileup functions only return the mismatches by positions.

Best
David


2013/4/5 Sean Davis <sdavis2@mail.nih.gov>

> On Tue, Mar 26, 2013 at 8:50 AM, David Greber <dav.greber@gmail.com>
> wrote:
> > Hello,
> >
> > How can I find the mismatching positions between a read (e.g. in a
> > "GappedAlignments" object) and the reference sequence (a "BSgenome"
> > object)? In general, I am looking for an operation that maps the read
> > sequence against the reference genome (taking cigar operation into
> account)
> > and compares the DNAString objects.
> >
> > I tried this, but due to the different cigar string operations, this
> seems
> > to become difficult for complex alignments. The "Rsamtools" package
> offers
> > with "cigarToIRangesListByAlignment", but does not take soft clips into
> > account.
> >
> > Is there some functionality in bioconductor for this? I assume that it
> is a
> > common task, but could not find anything like it.
>
> Hi, David.
>
> This doesn't answer your question directly, but you may want to look
> at pileup functionality in Rsamtools.  In particular, check out the
> applyPileups() function.
>
> Sean
>
>
> > Cheers
> > David
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

