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===        BEDTools        ===
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Created by Aaron Quinlan Spring 2009.
Copyright 2009 Aaron Quinlan. All rights reserved.
http://code.google.com/p/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 the ubiquitous UCSC Genome Browser BED format. 


===Manual===
See the extensive PDF manual included at: http://bedtools.googlecode.com/files/BEDTools-User-Manual.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/UsageMoreAdvanced



===BEDTools===

intersectBed			Returns overlaps between two BED files.
pairToBed				Returns overlaps between a paired-end BED file and a regular BED file.
pairToPair				Returns overlaps between two paired-end BED files.
bamToBed				Converts alignments in BAM format to BED or BEDPE format
windowBed				Returns overlaps between two BED files within a user-defined window.
closestBed				Returns the closest feature to each entry in a BED file.
subtractBed				Removes the portion of an interval that is overlapped by another feature.
mergeBed				Merges overlapping features into a single feature.
coverageBed				Summarizes the depth and breadth of coverage of features in one BED file versus genomic intervals defined in another.
genomeCoverageBed		Creates either a histogram or a "per base" report of genome coverage.
fastaFromBed			Creates FASTA sequences from intervals define in a BED file.
maskFastaFromBed		Mask a fasta file based on BED coordinates.
shuffleBed				Randomly permute the locations of a BED (-i) file among a genome.
slopBed					Adjust each BED entry by a requested number of base pairs.
sortBed					Sorts a BED file by genomic position or size.
linksBed				Creates an HTML file of links to the UCSC or a custom browser.
complementBed			Returns all genomic intervals not spanned by the features in a BED file.


===Installation===
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
6.  Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
7.  Use the tools.