[Bioperl-l] BEDTools module

Chris Fields cjfields at illinois.edu
Mon Jan 25 08:23:12 EST 2010


Great work Dan!  

chris

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).
> 
> cheers
> Dan
> 
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