Difference between revisions of "BEDTools"
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'''Example''': | '''Example''': | ||
If you want to sort the intervals in your .bed file you can do that by using following command | |||
bedtools sort -i input.bed | |||
== Documentation == | == Documentation == | ||
The full documentation can be found [http://bedtools.readthedocs.io/en/latest/index.html# here]. | The full documentation can be found [http://bedtools.readthedocs.io/en/latest/index.html# here]. | ||
Revision as of 11:59, 17 January 2017
Introduction
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
bedtools is developed in the Quinlan laboratory at the University of Utah and benefits from fantastic contributions made by scientists worldwide.
Installed version
The currently installed version is 2.26.0.
Using BEDtools with the HPC Cluster
If you want to find out more about BEDtools on the HPC Cluster, you can use the command
module spider bedtools
This will show you basic informations e.g. a short description and the currently installed version.
To load the desired version of the module, use the command
module load BEDTools/2.26.0-intel-2016b
Always remember: this command is case sensitive!
After loading the module, you can use the program with
bedtools <subcommand> [options]
Example:
If you want to sort the intervals in your .bed file you can do that by using following command
bedtools sort -i input.bed
Documentation
The full documentation can be found here.
