BLAT Results to BED for each Gene
0
0
Entering edit mode
6.2 years ago
gtasource ▴ 60

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!

blat • 1.2k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1466 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6