[BioC] Finding mismatches between reads and reference sequence

[Sean Davis]

On Tue, Mar 26, 2013 at 8:50 AM, David Greber <dav.greber at 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
>
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>
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