Hans-Ulrich,
We at the Hutch are currently adding support for alignments with indels
(I/D/S) and gaps (N) to Rsamtools in time for the BioC 2.6 release. What
functionality would you consider to be a must have for the BioC 2.6
release? We don't have a full spec for the release and your input, and
that of others, would be of great value to us.
Patrick
On 2/12/10 2:38 AM, Hans-Ulrich Klein wrote:
Dear All,
I am working with reads that have local alignments. That means, that
the reads only partially align to the reference. A read may also have
two or more subsequences that align to different positions. The BioC
class AlignedRead is not suitable in this situation. Also the
Rsamtools package does not support reads that have e.g. "D", "I" or
"S" within their cigar strings.
I would like to know whether someone has already implemented or
intends to add some functionality for local alignments.
Best wishes,
Hans-Ulrich
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
