[Bioperl-l] using Bio::DB::GFF for aggregation

Dan Kortschak dan.kortschak at adelaide.edu.au
Wed Jan 20 02:19:05 EST 2010


It doesn't really matter, they are largely inter-convertible. The
problem is not really the upstream processing, but the aggregation of
reads into read-assigned regions (unless I've misunderstood your
question).

Dan

On Tue, 2010-01-19 at 22:35 -0800, Jason Stajich wrote:
> Are you looking at the bowtie features file or the SAM?
> -jason
> On Jan 19, 2010, at 9:32 PM, Dan Kortschak wrote:
> 
> > Hi Chris (or others),
> >
> > I've been looking at ways to do large assemblies (really rnaseq/ 
> > readseq
> > comparisons for coverage) with maq/bowtie output and it's clear that  
> > for
> > the size of project that I'm working on the space complexity is too
> > nasty with Bio::DB::Sam. So I thought Bio::DB:GFF might be the way to
> > go.
> >
> > I was thinking: B:T:R:Bowtie ~> B:SeqFeat:Generic -> B:T:GFF ->  
> > B:DB:GFF
> >
> > This depends on the behaviour of B:DB:GFF->features(-merge=>1). I've
> > read through the docs, and it's not entirely clear (I'm hoping I've
> > interpreted it the right way), but does this result in the return of
> > features such that overlapping features are returned as a single  
> > feature
> > while non-overlapping features come back separately. If this is the
> > case, it would satisfy my requirements perfectly.
> >
> > thanks for your time
> > Dan
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> http://fungalgenomes.org/

-- 
Dan Kortschak <dan.kortschak at adelaide.edu.au>



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