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.

Cheers
David

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