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

Aaron Mackey ajmackey at gmail.com
Wed Jan 20 07:59:38 EST 2010


I would advise using BEDtools or the R IRanges package for this kind of
aggregation/merging work, rather than trying to reinvent this particular
wheel.

-Aaron

On Wed, Jan 20, 2010 at 12:32 AM, Dan Kortschak <
dan.kortschak at adelaide.edu.au> 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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