[Genome] Local BLAT

[Brooke Rhead]

Hi Mike,

If you run the blat command with no arguments, you will get a usage 
statement with instructions on how to run it, and an explanation of the 
available options.  If you have not already seen the BLAT specifications 
page, it should also be helpful:

http://genome.ucsc.edu/goldenPath/help/blatSpec.html

 > For instance, can I use the
 > 'mm8.2bit' file as-is for the database, like:
 >
 > blat mm8.2bit my_sequences.2bit [-ooc=11.ooc] output.psl
 >
 > Or do I need to do something to create the index first?

You could use that command.  Using the .ooc file is optional.  As you 
will see in the BLAT instructions, the query sequence and the database 
sequence can be in either .2bit or .fa format, so you can use whichever 
format is convenient for you.

You do not need to build an index first if you are using blat (you do 
with gfServer/gfClient).  From the blat specifications page: "blat 
–combines client and server into a single program, first building the 
index, then using the index, and then exiting."

 > Also, since my machine is pretty modest (768MB RAM), would it be
 > better to break up the database and do the BLATs one chromosome at a
 > time?

BLAT should tell you if it is out of RAM by giving an error.  Since you 
have less than 1GB, you may need to blat the chromosomes separately.

You can either split up the the mm8.2bit file into chromosomes (using 
the tool 'twoBitToFa', included in the BLAT suite), or you can simply 
use the .fa formatted sequence, which is already available as 
one-file-per-chromosome, here:

http://hgdownload.cse.ucsc.edu/goldenPath/mm8/bigZips/chromFa.tar.gz

I hope this information helps.  Please feel free to write back to this 
list if you have further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Michael Mooney wrote:
> Hi, 
> 
> I need to align a large number (thousands) of sequences to the genome,
> so I'm trying to set up a local copy of BLAT on my machine. I've
> downloaded the linux executables and the 'mm8.2bit' data file, and I'm
> wondering what the next step is. Are there more detailed instructions
> than what I've been able to find on the web? For instance, can I use the
> 'mm8.2bit' file as-is for the database, like: 
> 
>> blat mm8.2bit my_sequences.2bit [-ooc=11.ooc] output.psl 
> 
> Or do I need to do something to create the index first? 
> 
> Also, since my machine is pretty modest (768MB RAM), would it be better
> to break up the database and do the BLATs one chromosome at a time? 
> 
> Thanks very much, 
> 
> Mike 
> 
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