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

Jason Stajich jason at bioperl.org
Wed Jan 20 01:35:24 EST 2010


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
>
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/



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