PSL to BED?

[Azazel]

How can I convert output from Jim Kent's BLAT, which is in PSL format, into BED format?

[AlexReynolds]

I have posted a new psl2bed conversion script to an unstable development branch of our BEDOPS suite, which you can download as follows:

$ svn checkout http://bedops.googlecode.com/svn/branches/v2p1p0 bedops_v2p1p0
$ cd bedops_v2p1p0
$ make
$ make install
$ cd bin
$ ./psl2bed --help

This script will convert headerless (default) and headered PSL files by moving columns around into BED output that follows UCSC BED format conventions, up to the first six columns. Remaining fields are mapped to columns 7 through 21.

Run psl2bed --help for a more complete description.

As an example, here is how to make a sorted BED file called sorted-foo.bed, converted from a headered PSL file called foo.psl:

$ psl2bed --headered < foo.psl > sorted-foo.bed

This relies on installing BEDOPS binaries, including psl2bed and sort-bed in a location accessible through your PATH environment variable.

Note that this is a development branch, so there are no guarantees that versions of BEDOPS apps made from this branch are stable. These and other improvements will end up in the final v2.1 release of BEDOPS, hopefully in a month or two.

[AlexReynolds]

We have put out a "final" release of BEDOPS v2.1 here, which includes the psl2bed script.