[Genome] Question about Blat

[Donna Karolchik]

Andy,

This is how the web-based Blat score is calculated:

int pslScore(const struct psl *psl)
/* Return score for psl. */
{
return psl->match + (psl->repMatch>>1) - psl->misMatch - psl->qNumInsert
  - psl->tNumInsert;
}

We use a number of different scoring schemes for different purposes. The psl
files that Blat produces therefore end up not having scores, but rather the
raw materials for calculating scores a number of different ways.

-Donna

----- Original Message -----
From: "Donna Karolchik" <donnak at soe.ucsc.edu>
To: <Andrew.Fortna at uchsc.edu>; <genome at soe.ucsc.edu>
Sent: Wednesday, January 28, 2004 3:20 PM
Subject: Re: [Genome] Question about Blat


> Andy,
>
> Try adding -minScore=0 -minIdentity=0 to gfClient.
>
> -Donna
> -----------------------------------
> Donna Karolchik
> UCSC Genome Bioinformatics Group
> donnak at soe.ucsc.edu
>
> ----- Original Message -----
> From: <Andrew.Fortna at uchsc.edu>
> To: <genome at soe.ucsc.edu>
> Sent: Wednesday, January 28, 2004 10:46 AM
> Subject: [Genome] Question about Blat
>
>
> > Hello,
> >
> > I was wondering if you can tell me exactly how the score is determined
> with the web-based version BLAT?  I was initially using the web-based BLAT
> and using the score as part of a cutoff requirement.  Now I'm using a
> locally installed version of BLAT on a Solaris machine and I can't quite
> figure out how to calculate the score in the same manner as is done for
the
> web-based version.
> >
> > Thank you very much,
> > Andy Fortna
> >
> >
> > _______________________________________________
> > Genome maillist  -  Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> >
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>