BLAT Results to BED for each Gene

Question

[gtasource]

Hi guys,

I have the results from my BLAT search, where I used BLAT to search a list of genes against a reference fasta. I now have a huge list of results and coordinates for each gene against this reference. What I want to do now is to take the best match (or the longest) for each of these genes, and put them into a bed file.

I guess, my question is:

1.) How do I go about finding the "best" match (can I consider the longest the best?) 2.) I was thinking of writing a simple script that looks at all of the gene matches, and takes the line that has the largest match.

Any input would be great!

[GenoMax]

What format is the blat output in? If you had used the default PSL format it should be easy to convert it to BED.