[Bioperl-l] BEDTools module

Dan Kortschak dan.kortschak at adelaide.edu.au
Mon Jan 25 00:33:28 EST 2010


Hi All,

A wrapper and parser for the BEDTools utilities suite of Aaron Quinlan
and Ira Hall is now available in the bioperl-run subversion repository
(bioperl-run/trunk r16754).

Using BEDTools you can, among other things:

      * Intersecting two BED files in search of overlapping features.
      * Merging overlapping features.
      * Screening for paired-end (PE) overlaps between PE sequences and
        existing genomic features.
      * Calculating the depth and breadth of sequence coverage across
        defined "windows" in a genome.

(see <http://code.google.com/p/bedtools/> for manuals and downloads).

BEDTools is a suite of 17 commandline executable. The module attempts to
provide and options comprehensively and can return Bio::SeqIO or
Bio::SeqFeature::Collection object where appropriate (or Bio::Root::IO
where specific handling has not been implemented - please give feedback
on desired features for this).

cheers
Dan



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