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author aaronquinlan
date Sat, 19 Nov 2011 14:17:03 -0500
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1 ==============================
2 BEDTools
3 ==============================
4
5 Created by Aaron Quinlan Spring 2009.
6
7 Copyright 2009,2010,2011 Aaron Quinlan. All rights reserved.
8
9 Stable releases: http://code.google.com/p/bedtools
10
11 Repository: https://github.com/arq5x/bedtools
12
13 Released under GNU public license version 2 (GPL v2).
14
15
16 Summary
17 -------
18 BEDTools is a collection of utilities for comparing, summarizing, and
19 intersecting genomic features in BED, GTF/GFF, VCF and BAM formats.
20
21
22 Manual
23 ------
24 See the extensive PDF manual included at: http://code.google.com/p/bedtools/downloads/detail?name=BEDTools-User-Manual.v4.pdf.
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26 This manual covers many common usage examples. There are also examples available at:
27 http://code.google.com/p/bedtools/wiki/Usage
28 http://code.google.com/p/bedtools/wiki/UsageAdvanced
29
30 Installation
31 ------------
32 Git
33 ...
34 git clone git://github.com/arq5x/bedtools.git
35
36 Download tarball - that big gray button on the upper right.
37 ...........................................................
38 #. Unpack the source downloaded tarball.
39 #. cd into the expanded folder.
40 #. Type "make clean" and hit enter.
41 #. Type "make all" and hit enter.
42 #. If you encountered no errors, then all of the BED Tools should now be in bin/
43 If not, try to troubleshoot then email me: aaronquinlan at gmail dot com
44 #. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
45 #. Use the tools.
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47