[Genome] help with blat

[Galt Barber]

The usage in blat documentation of the word "database"
is very loose.  We don't mean something like
Oracle, MySQL or Postgres, etc.  We do mean
a genome in the form of a .fa, .nib, or .2bit.

-Galt


On Fri, 18 Apr 2008, Ann Zweig wrote:

> Hello Thomas,
>
> 	Here is a detailed specification describing the Blat program:
> http://genome.ucsc.edu/goldenPath/help/blatSpec.html
>
> 	As you likely know, you will also need to download the alignments for
> the genome you are interested in.  Navigate to our download sever:
> http://hgdownload.cse.ucsc.edu/downloads.html  Then press the name of
> the organism you are interested in, then then press the "Data set by
> chromosome" link.  These are the fa files per chromosome for that
> assembly.  Read the blatSpec.html file to determine how to prepare these
> files for use with your stand-alone Blat.
>
> 	You might also find the BLAT section of our FAQ useful:
> http://genome.ucsc.edu/FAQ/FAQblat
>
> 	If, after reading through these resources, you still have questions,
> please don't hesitate to contact the mail list again.
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
> Please feel free to search the Genome mailing list archives by visiting
> our home page, clicking on "Contact Us", then typing a word or phrase
> into the search box.  On that same page
> (http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome
> mailing list.
>
>
>
>
> Thomas Nicholas wrote:
> > I just downloaded and installed your blatSuite 34 to my machine, but
> > I am having trouble figuring out the parameters to make it run.  I
> > have a database that I want to use that I generated using formatdb
> > and I have several fasta sequences that I want to blat search.  I
> > have tried to enter the database into the -t option and the fastas
> > into the -q, but that is still not working.  Could you please let me
> > know how to enter in my database, query, and output into the command
> > line?  Thanks.
> >
> > Thomas Nicholas
> > _______________________________________________
> > 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
>