[Bioc-sig-seq] locally aligned reads

Martin Morgan mtmorgan at fhcrc.org
Fri Feb 12 18:22:25 CET 2010


On 02/12/2010 06:28 AM, Patrick Aboyoun wrote:
> 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.

For what it's worth, Rsamtools scanBam does currently input these reads;
the cigar is a factor and interpretable by the end user; as Patrick says
things are in the works for much richer support. Martin


>>
>> I would like to know whether someone has already implemented or
>> intends to add some functionality for local alignments.
>>
>> Best wishes,
>> Hans-Ulrich
>>
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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