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=== BEDTools ===
Created by Aaron Quinlan Spring 2009.
Copyright 2009 Aaron Quinlan. All rights reserved.
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http://code.google.com/p/bedtools
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Released under GNU public license version 2 (GPL v2).
BEDTools is a collection of utilities for comparing, summarizing, and
intersecting genomic features in the ubiquitous UCSC Genome Browser BED format.
===Manual===
See the PDF manual included in this distribution for more details on usage, file formats, behavior, etc.
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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
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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.
1. Unpack the source downloaded tarball.
2. cd into the expanded folder.
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.