Bed Tools User-manual.v4.pdf

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Created by Aaron Quinlan Spring 2009.

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

User Manual Pdf

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

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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.

Bed Tools User-manual.v4.pdf Free

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

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
  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.