Quick start

Install BEDTools

curl http://bedtools.googlecode.com/files/BEDTools.<version>.tar.gz > BEDTools.tar.gz
tar -zxvf BEDTools.tar.gz
cd BEDTools
make clean
make all
sudo cp bin/* /usr/local/bin/

Use BEDTools

Below are examples of typical BEDTools usage. Additional usage examples are described in section 6 of this manual. Using the “-h” option with any BEDTools will report a list of all command line options.

A. Report the base-pair overlap between the features in two BED files.

intersectBed -a reads.bed -b genes.bed

B. Report those entries in A that overlap NO entries in B. Like “grep -v”

intersectBed -a reads.bed -b genes.bed ?Cv

C. Read BED A from stdin. Useful for stringing together commands. For example, find genes that overlap LINEs but not SINEs.

intersectBed -a genes.bed -b LINES.bed | intersectBed -a stdin -b SINEs.bed ?Cv

D. Find the closest ALU to each gene.

closestBed -a genes.bed -b ALUs.bed

E. Merge overlapping repetitive elements into a single entry, returning the number of entries merged.

mergeBed -i repeatMasker.bed -n

F. Merge nearby repetitive elements into a single entry, so long as they are within 1000 bp of one another.

mergeBed -i repeatMasker.bed -d 1000