[Genome] blat output

[Ann Zweig]

Hello Jimmy,

	From your question it sounds like you are using stand-alone BLAT.  To 
replicate the web-based BLAT parameters, see this FAQ: 
http://genome.ucsc.edu/FAQ/FAQblat#blat5

	If you download some tools from our source code, you will be able to 
set up your output to look like the output on the website.

	The Genome Browser and Blat software are free for academic, nonprofit, 
and personal use. A license is required for commercial use.

How to download the software: 
http://genome.cse.ucsc.edu/FAQ/FAQlicense#license3

You can obtain the source tree either via CVS:
	http://genome.ucsc.edu/admin/cvs.html
or a zip file:
	http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

Please note the build instructions:
	http://genome.ucsc.edu/admin/jk-install.html

	All of the kent utilities output their usage message and command
line options by running them with no arguments.


1. Run stand-alone BLAT to get psl output.
2. use pslPretty on the psl output plus the 2bit files to get the 
sequence alignment picture that you are looking for.

pslPretty - Convert PSL to human readable output
usage:
    pslPretty in.psl target.lst query.lst pretty.out
options:
    -axt - save in something like Scott Schwartz's axt format
           Note gaps in both sequences are still allowed in the
           output which not all axt readers will expect
    -dot=N Put out a dot every N records
    -long - Don't abbreviate long inserts
    -check=fileName - Output alignment checks to filename
It's a really good idea if the psl file is sorted by target
if it contains multiple targets.  Otherwise this will be
very very slow.   The target and query lists can either be
fasta, 2bit or nib files, or a list of fasta, 2bit and/or nib files
one per line


Regards,

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

	

JIMMY LIN wrote:
> Instead the standard -out specifications (e.g. psl, pslx, axt, maf, wublast, blast), I would like to have the output format from the website (i.e. after clicking on the details on the hyperlink --> cDNA, genome, and alignment).
> 
> Specifically, I am interested in the CDA format with the upper and lowercase to indicate match. Is source code available?
> 
> Thanks,
> Jimmy
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