[Genome] help with blat

[Hiram Clawson]

Good Morning Thomas:

The blat program doesn't need a database.  It takes two arguments,
the target sequence, and the query sequence.  Run the blat command
without any arguments and it will print out its help message and
command line syntax.

The target and query sequence can be fasta files, or more efficiently
can be 2bit files.  2bit files can be made from fasta files with
the faToTwoBit command.

--Hiram

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