Commit ebbbd305 authored by Aaron's avatar Aaron
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Revising README to README.rst

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==============================
=== BEDTools ===
==============================
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.
==============================
BEDTools
==============================
Created by Aaron Quinlan Spring 2009.
Copyright 2009,2010,2001 Aaron Quinlan. All rights reserved.
Stable releases: http://code.google.com/p/bedtools
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, and
intersecting 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/Usage
http://code.google.com/p/bedtools/wiki/UsageAdvanced
Installation
------------
#. Unpack the source downloaded tarball.
#. cd into the expanded folder.
#. Type "make clean" and hit enter.
#. Type "make all" and hit enter.
#. 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
#. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
#. Use the tools.
List of available tools
-----------------------
*Utility* *Description*
========================= ====================================================
*intersectBed (BAM)* Returns overlaps between two BED/GFF/VCF files.
*pairToBed (BAM)* Returns overlaps between a paired-end BED file and a
regular BED/VCF/GFF file.
*bamToBed (BAM)* Converts BAM alignments to BED6, BED12,
or BEDPE format.
*bedToBam (BAM)* Converts BED/GFF/VCF features to BAM format.
*bed12ToBed6* Converts "blocked" BED12 features to discrete
BED6 features.
*bedToIgv* Creates IGV batch scripts for taking multiple
snapshots from BED/GFF/VCF features.
*coverageBed (BAM)* Summarizes the depth and breadth of coverage of features in one BED versus features
(e.g, "windows", exons, etc.) defined in another BED/GFF/VCF file.
*genomeCoverageBed (BAM)* Creates either a histogram, BEDGRAPH, or a "per base" report of genome coverage.
*unionBedGraphs* Combines multiple BedGraph files into a single file, allowing coverage/other comparisons between them.
*annotateBed* Annotates one BED/VCF/GFF file with overlaps from many others.
*groupBy* Summarizes data in a file/stream based on common columns.
*overlap* Returns the number of bases pairs of overlap b/w two features on the same line.
*pairToPair * Returns overlaps between two paired-end BED files.
*closestBed* Returns the closest feature to each entry in a BED/GFF/VCF file.
*subtractBed* Removes the portion of an interval that is overlapped by another feature.
*windowBed (BAM)* Returns overlaps between two BED/VCF/GFF files based on a user-defined window.
*mergeBed* Merges overlapping features into a single feature.
*complementBed* Returns all intervals _not_ spanned by the features in a BED/GFF/VCF file.
*fastaFromBed* Creates FASTA sequences based on intervals in a BED/GFF/VCF file.
*maskFastaFromBed* Masks a FASTA file based on BED coordinates.
*shuffleBed* Randomly permutes the locations of a BED file among a genome.
*slopBed* Adjusts each BED entry by a requested number of base pairs.
*sortBed* Sorts a BED file by chrom, then start position. Other ways as well.
*linksBed* Creates an HTML file of links to the UCSC or a custom browser.
========================= =======================================================================================================
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