[Genome] can we set a maximum score upper bound for BLAT

[Galt Barber]

There is no maxScore.
People typically use pslReps and pslCDnaFilter
to post-filter blat psl results.
However all of these are aimed at finding
the best quality matches.  Lower-scoring alignments
are typically plentiful, and people usually are trying
to filter them OUT.

I think you could write a simple script that would
look at coverage and percent identity and you could
filter out for example exact matches.

Good luck!

-Galt


On Thu, 17 Apr 2008, Mera Vigyan wrote:

> I am a student from Italy.  I am using BLAT to know homology about genome
> data.  Just llike "minScore", Can we set a parameter or fixing an maximum
> score upper bound for BLAT ?
> I want to run BLAT on a huge chunks of data with a maximum score upper
> bound.  how to do that ?
>
> thanks
> Swaminathan
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>