@@ -12,6 +12,21 @@ Free for non-profit or academic use.
BEDTools, prosaic as it may be, is a collection of utilities for comparing and
intersecting genomic features in the UCSC Genome Browser BED format.
===BEDTools===
intersectBed --- returns overlaps between two BED files.
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.
windowBed --- returns overlaps between two BED 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 file.
fastaFromBed --- creates FASTA sequences based on intervals in a BED file.
coverageBed --- creates a BED graph file based on the the overlaps of two BED files.
genomeCoverageBed --- creates either a histogram or a "per base" report of genome coverage.
sortBed --- sorts a BED file by chrom, then start position.
linksBed --- creates an HTML file of links to the UCSC or a custom browser.
===Installation===
1. If you are reading this, you successfully downloaded and unzipped/unpacked the source tarball. Great.
2. Type "make all" at the command line.
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@@ -47,7 +62,7 @@ Royden is the resident UCSC browser expert. He has helped me immensely by teach
browser. Also, the algorithmic concept behind the genomeCoverageBed program is Royden's.
6. Fitz Elliot, UVa
Fitz kindly taught me the ways of version control with git. For those of who that are constantly confused by CVS and SVN, try git. I think you'll be happy.
Fitz kindly taught me the ways of version control with git. For those that are constantly confused by CVS and SVN, try git. I think you'll be happy.
7. Loyal Goff, CSAIL, Broad.
Many thanks to Loyal for his assistance in making BED Tools "compilable" on the SUSE platform. I appreciate your help and patience.
