[Genome] blat: minIdentity option not working?

[Adnan Derti]

Hi.

I'm using blat (v. 31x1) locally to align mouse and human mRNAs to their 
respective genomes. Blat produces aligned segments with <90% identity 
whether I use the default options or specify -minIdentity=90. I use 
-out=blast8 and haven't checked whether other output options produce the 
same results. Am I misunderstanding the way -minIdentity should work?

Thanks.

Adnan Derti