Bed Tools User-manual.v4.pdf

Created by Aaron Quinlan Spring 2009.

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.

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

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

Bed Tools User-manual.v4.pdf Download

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, andintersecting 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/Usagehttp://code.google.com/p/bedtools/wiki/UsageAdvanced

Installation

Git

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

User Manual Pdf

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' and hit enter.
  4. If you encountered no errors, then bedtools should now be in bin/
If not, try to troubleshoot then email me: aaronquinlan at gmail dot com
Tools

Bed Tools User-manual.v4.pdf Free

  1. Run the test suite with: 'make test'
  2. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin. Make sure that the directory to which you copy the tools is in your $PATH
  3. Use the tools.