Hi Hans-Ulrich,
An update on this. We've recently added the GenomicRanges package
to BioC devel.
Description: The ability to efficiently store genomic annotations and
alignments is playing a central role when it comes to analyze
high-throughput sequencing data (a.k.a. NGS data). The package
defines general purpose containers for storing genomic intervals
as well as more specialized containers for storing alignments
against a reference genome.
In particular it provides a class (GappedAlignments) that is suitable
for storing alignments with deletions, insertions and/or gaps. Note
that it's a light-weight class in the sense that it doesn't store the
query sequences. Right now the mismatch information isn't stored either
but we might consider adding it in the future based on the feedback we
receive.
Please give GenomicRanges a try when you get a chance. It's still very
much a work-in-progress (as the version indicates -- 0.0.9) but you
can already perform some useful operations like coverage(),
findOverlaps(), etc... on your GappedAlignments/GRanges/GRangesList
objects.
Your feedback we'll be very appreciated.
Cheers,
H.
PS: At this moment you still need to install Rsamtools directly from
Subversion in order to be able to load a BAM file into a
GappedAlignments object with readGappedAlignments().
Martin Morgan wrote:
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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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
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