Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing, communications and informatics.

Bedops

 

Bedops is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets — BEDOPS aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

Installed on blacklight

Other resources that may be helpful include:

Shane Neph, M. Scott Kuehn,
Alex P. Reynolds, Eric Haugen, Robert E. Thurman, Audra K. Johnson, Eric Rynes,
Matthew T. Maurano, Jeff Vierstra, Sean Thomas, Richard Sandstrom, 
Richard Humbert,and John A. Stamatoyannopoulos
BEDOPS: high-performance genomic feature operations
Bioinformatics (2012) 28 (14): 1919-1920
doi:10.1093/bioinformatics/bts277
Website: http://code.google.com/p/bedops/ 

Running bedops

1) Make the bedops commands availiable for use

a) blacklight
The bedops programs will be made availiable for use through the module command. To load the bedops module enter:

module load bedops

2) Programs in the bedops package:

bedextract --Efficiently extracts features from BED input.
bedmap --Maps source signals from map-file onto qualified target regions from ref-file. Calculates an output for every ref-file element.
bedops --Offers set and multiset operations for files in BED format.
closest-features --For every element in input-file, find those elements in query-file nearest to its left and right edges.
sort-bed --Sorts input BED file(s) into the order required by other utilities. Loads all input data into memory.
starch --Lossless compression of any BED file.
unstarch --Decompression of a starch archive.
starchcat --Merge multiple starch archive inputs into one starch archive output.

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