Question: BLAT Results to BED for each Gene
gravatar for gtasource
16 months ago by
gtasource30 wrote:

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 • 338 views
ADD COMMENTlink written 16 months ago by gtasource30

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 REPLYlink written 16 months ago by genomax76k
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