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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. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

From the BEDOPS website:

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

The suite includes tools for set and statistical operations (bedops, bedmap and closest-features) and compression of large inputs into a novel lossless format (starch) that can provide greater space savings and faster data extractions than current alternatives. BEDOPS offers native support for this deep compression format, in addition to BED.

BEDOPS also offers logarithmic time search to per-chromosome regions in sorted BED data (in bedextract and core BEDOPS tools). This feature makes whole-genome analyses “embarassingly parallel”, in that per-chromosome computations can be distributed onto separate work nodes, with results collated at the end in map-reduce fashion.

Sorting arbitrarily large BED files is easy with sort-bed, which easily scales beyond available system memory, as needed. We also offer portable conversion scripts that transform data in common genomic formats (SAM/BAM, GFF/GTF, PSL, WIG, and VCF) to sorted BED data that are ready to use with core BEDOPS utilities.

All of these tools are made to be glued together with common UNIX input and output streams. This helps make your pipeline design and maintenance easy, fast and flexible.

Operation Example:

Element-of (-e, –element-of)
The --element-of operation shows the elements of the first (“reference”) file that overlap elements in the second and subsequent “query” files by the specified length (in bases) or by percentage of length.

In the following example, we search for elements in the reference set A which overlap elements in query set B by at least one base:


Elements that are returned are always from the reference set (in this case, set A).

The argument to --element-of is a value that species to degree of overlap for elements. The value is either integral for per-base overlap, or fractional for overlap measured by length.

Here is a demonstration of the use of --element-of 1 on two sorted sets First.bed and Second.bed, which looks for elements in the First set that overlap elements in the Second set by one or more bases:

$ more First.bed
chr1      100     200
chr1      150     160
chr1      200     300
chr1      400     475
chr1      500     550

$ more Second.bed
chr1      120     125
chr1      150     155
chr1      150     160
chr1      460     470
chr1      490     500
$ bedops --element-of 1 First.bed Second.bed > Result.bed

$ more Result.bed
chr1      100     200
chr1      150     160
chr1      400     475


Learn more from the excellent BEDOPS documentation.
 

The BioGrids Installer is an easy to use application that makes installing and managing life sciences software simple and quick.
 

 

curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Linux.tgz
tar zxf biogrids-1.0.694-Linux.tgz
cd biogrids-1.0.694-Linux

curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Darwin.tgz
tar zxf biogrids-1.0.694-Darwin.tgz
cd biogrids-1.0.694-Darwin

./biogrids activate biogrid-production jvinent1  70rYFTDnmCr93VUklfbf1s3M4jdyC9bFVYHew==

Replace the site name, user name and activation key with your own credentials.

./biogrids install fastqc trimmomatic samtools star subread igv

./biogrids installed