[Bioperl-l] BEDTools module
cjfields at illinois.edu
Mon Jan 25 08:23:12 EST 2010
Great work Dan!
On Jan 24, 2010, at 11:33 PM, Dan Kortschak wrote:
> 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).
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