[Genome] Need some help

[Ann Zweig]

Scott-

	Now I understand.  You are correct in remembering that the on line BLAT 
program only allows 25 sequences at a time.  What will be helpful to you 
is your own BLAT executable.  Read about getting a copy of the BLAT 
source here: http://genome.ucsc.edu/FAQ/FAQblat.html#blat3.    For 
non-commercial users like yourself no license is required.  Once you
have that installed on your machine, you can type 'blat' at the 
command-line to see the usage statement for the tool.

	The tool will provide you with an output file containing the best hits 
for each sequence.  After you get the output, you may want to filter out 
on the best few hits (or best single hit) for each sequence.  You can do 
this using the pslCDnaFilter tool.  This tool requires alignments that 
have the repMatch psl field set even when doing alignments without 
masking.  The command line blat option -repeats=lower enables counting 
repeat matches.

	Read about how to download the pslCDnaFilter tool from our source code 
here: http://genome.ucsc.edu/FAQ/FAQlicense#license3.  You will find the 
tool here: /cluster/bin/i386/pslCDnaFilter.

	You will find another filtering tool (called pslReps) in the same 
location in the source tree that will provide you only the single best 
match (or within X% of best).  As with the BLAT tool, simply type the 
name of the tool at the command line with no parameters to see the usage 
statement.


Hope this is helpful.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

Hebbring, Scott J. wrote:
> You are on the right track.  I want to use the short sequence fragments from "chrN_random.fa.gz" (about 2000 sequences) and blat these across the genome.  If I recall, I can only blat 25 sequences at one time.  Is there a faster way?  I would like to do this under the assumption that one of these fragments might not be aligning because it falls on one of the breakpoints of my deletion/duplication.
> 
> Thanks for the help
> Scott Hebbring 
> 
> -----Original Message-----
> From: Ann Zweig [mailto:ann at soe.ucsc.edu] 
> Sent: Wednesday, March 01, 2006 4:57 PM
> To: Hebbring, Scott J.
> Cc: 'genome at soe.ucsc.edu'
> Subject: Re: [Genome] Need some help
> 
> Hello Scott-
> 
> 	I am a little unclear on exactly what you are asking, but let me take a 
> stab at it.
> 
> 	I think that you would like to BLAT the fragments of gene that you get 
> when you break it at these breakpoints to see where they align on the 
> genome.  Do you already have these sequence fragments?  If so, then you 
> would want to BLAT and then do some sort of filtering to get the best 
> hits.  From those results, you could make a custom track and or do Table 
> Browser queries.
> 
> 	If I am on the right track, let me know and I'll point you towards some 
> tools that may be helpful.  If not, please re-explain your problem.  Thanks.
> 
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> 
> Hebbring, Scott J. wrote:
> 
>>For background, I have a gene that is polymorphicly duplicated and deleted.  I wanted to try and use chr?_random.fa.gz sequence from your site to help map the break points.  Is there a good way to download these fragments as a custom track or to input these sequences in the Table browser?  In a sense, I want to do a BLAT of 2,000 small sequences.
>>Thanks
>>Scott Hebbring
>>
>>_______________________________________________
>>Genome maillist  -  Genome at soe.ucsc.edu
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