quick-start.rst

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
sudo cp bin/* /usr/local/bin/

Use bedtools

Below are examples of typical bedtools usage. Using the "-h" option with any bedtools will report a list of all command line options.

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

bedtools intersect -a reads.bed -b genes.bed

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

bedtools intersect  -a reads.bed -b genes.bed

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

bedtools intersect -a genes.bed -b LINES.bed | \
  bedtools intersect -a stdin -b SINEs.bed -v

Find the closest ALU to each gene.

bedtools closest -a genes.bed -b ALUs.bed

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

bedtools merge -i repeatMasker.bed -n

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

bedtools merge -i repeatMasker.bed -d 1000