Finding The Best Hit From Blat Output For A Microsatellite

Question

[figo]

Hi All

I have a repeat element sequence (Microsatellite) and I want look this element in the entire genome of a mammal which has been assembled as scaffolds. I ran BLAT on this and got around 9000 hits. Now I want to extract the best hits from the .psl file. As some of the hits are on same scaffolds, how I can filter the best hit from this? .Is there a script or program to do this.

Regards

Answer 1

[Shaojiang Cai]

I would recommend Microsoft Excel, seriously.

Because best hits is your criteria, there may not be such a script tailored for you.

By sorting the # of matches or # of matches / total length, you can get the hits with longest alignment lengths. Or sorting by the starting position of the reference sequence, you can view hits on some contig based on positions. Please check the PSL format.