jakebiesinger / bedtools

A powerful toolset for genome arithmetic.

BEDTools

Created by Aaron Quinlan Spring 2009.

Copyright 2009,2010,2011 Aaron Quinlan. All rights reserved.

Stable releases: http://code.google.com/p/bedtools

Repository: https://github.com/arq5x/bedtools

Released under GNU public license version 2 (GPL v2).

Summary

BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in BED, GTF/GFF, VCF and BAM formats.

Manual

See the extensive PDF manual included at: http://code.google.com/p/bedtools/downloads/detail?name=BEDTools-User-Manual.v4.pdf.

This manual covers many common usage examples. There are also examples available at: http://code.google.com/p/bedtools/wiki/Usage http://code.google.com/p/bedtools/wiki/UsageAdvanced

Installation

Git

git clone git://github.com/arq5x/bedtools.git

Download tarball - that big gray button on the upper right.

1. Unpack the source downloaded tarball.
2. cd into the expanded folder.
3. Type "make clean" and hit enter.
4. Type "make all" and hit enter.
5. If you encountered no errors, then all of the BED Tools should now be in bin/

If not, try to troubleshoot then email me: aaronquinlan at gmail dot com

1. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
2. Use the tools.