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

[Mera Vigyan]

greetings,

I am having BLAT output in blast8 format, so i cant use pslReps or
pslCDnaFilter, isnt it ?.  This format is a sorted in the descending order
of score, isnt it?  If i pick up the first lines of the output, it
corresponds to the best blat hits for the particular query sequence.

The query sequences have lengths of about 700 bps.  Then can I run the blat
with minScore of 300.   I did an experiment with chunk of 50000 query
sequences. I ran blat with only parameter of  -out=blast8 format. But still
I find that  the output contains data pertaining to 49603 sequences only.
why is this ? as i havent specified -minScore or any other parameters.
So, how can i get the blat output for the full set of sequences.

thanks



On Fri, Apr 18, 2008 at 7:32 PM, Galt Barber <galt at soe.ucsc.edu> wrote:

>
> from http://genome.ucsc.edu/FAQ/FAQblat#blat8
>
> A note on filtering output: increasing the -minScore parameter value
> beyond one-half of the query size has no further effect. Therefore, use
> either the pslReps or pslCDnaFilter  program available in the Genome
> Browser source code to filter for the size, score, coverage, or quality
> desired.
>
> ---
>
> It seems that blat sometimes will output an alignment
> that it thinks is pretty good, even if it doesn't
> meet minScore setting. Therefore best not to rely
> entirely on -minScore.
>
> -Galt
>
>
> On Fri, 18 Apr 2008, Mera Vigyan wrote:
>
> > Thank you Galt
> > I am a beginner, I have a rather naive question.. that is suppose I run
> BLAT
> > with a -minScore-600. It means that the results will have all their
> contents
> > above this
> > cutoff isnt it?
> >
> > my command line :  blat -minScore=600 -out=blast8
> > this means that each every  value from the output  in the right most
> score
> > column,  should be  greater than 600.
> > None of the output score values can be less than 600.
> > isnt it so?
> >
> > thanks again
> >
> >
> >
> >
> >
> > On Thu, Apr 17, 2008 at 8:03 PM, Galt Barber <galt at soe.ucsc.edu> wrote:
> >
> > >
> > > 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
> > > >
> > >
> >
>