User: David Greber

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David Greber30
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Posts by David Greber

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Answer: A: Finding mismatches between reads and reference sequence
... Hi Herve, Thank you for the nice and comprehensive example. I will check it out and will try to incorporate also insertions. Best David 2013/4/5 Hervé Pagès > Hi David, > > Sorry for the delay in answering this. Was too busy trying to get > a few things done before the new BioC re ...
written 6.0 years ago by David Greber30
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Comment: C: Finding mismatches between reads and reference sequence
... 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 > On Tue, Mar 26, 2013 at 8:50 AM, David Greb ...
written 6.0 years ago by David Greber30
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Finding mismatches between reads and reference sequence
... 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 compare ...
written 6.0 years ago by David Greber30

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