(Paired-End Bam to BED12 modified) BEDTools
Addition of a pairedBamToBed12 utility by Nicolas Bertin (OSC RIKEN Yokohama) to BEDTools Created by Aaron Quinlan Spring 2009.
Copyright 2009,2010,2011 Aaron Quinlan. All rights reserved. Released under GNU public license version 2 (GPL v2).
BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in BED, GTF/GFF, VCF and BAM formats. In this branch is added pairedBamToBed12 which converts a name sorted paired-end sequences bam file into a 2-block bed12 formatted file.
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 Note that the manual does not reflect the pairedBamToBed12 addition.
- 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
|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.|
|pairedBamToBed12||Convert a name sorted paired-end sequences bam file into a 2-block bed12 formatted file.|