[Bioperl-l] BEDTools module
dan.kortschak at adelaide.edu.au
Mon Jan 25 00:33:28 EST 2010
A wrapper and parser for the BEDTools utilities suite of Aaron Quinlan
and Ira Hall is now available in the bioperl-run subversion repository
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).
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