[Genome] Looking for g2gOverlap and other BLAT-associated programs

[Hiram Clawson]

Good Morning David:

We do not package the hundreds of kent source tree utilities.
http://genome.ucsc.edu/license/
http://genomewiki.ucsc.edu/index.php/Kent_source_utilities

You can fetch and build the entire source tree:
http://genome.ucsc.edu/admin/cvs.html
or: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
http://genome.ucsc.edu/admin/jk-install.html

And the program you are looking for is in the source directory:
	src/hg/gigAssembler/g2gOverlap/
although you may be looking for the newer program: pslFilter
which is in src/hg/pslFilter/

--Hiram

$ pslFilter
pslFilter - filter out psl file
     pslFilter in.psl out.psl
options
     -dir  Input files are directories rather than single files
     -reward=N (default 1) Bonus to score for match
     -cost=N (default 1) Penalty to score for mismatch
     -gapOpenCost=N (default 4) Penalty for gap opening
     -gapSizeLogMod=N (default 1.00) Penalty for gap sizes
     -minScore=N (default 15) Minimum score to pass filter
     -minMatch=N (default 30) Min match (including repeats to pass)
     -minUniqueMatch (default 20) Min non-repeats to pass)
     -maxBadPpt (default 700) Maximum divergence in parts per thousand
     -minAli (default 600) Minimum ratio query in alignment in ppt
     -noHead  Don't output psl header
     -minAliT (default 0) Like minAli for target

David Gloriam wrote:
> Hi,
> 
> I found a number of useful BLAT-associated programs in this document in the
> downloads section:
> 
> http://genome-test.cse.ucsc.edu/~kent/exe/usage.txt
> 
> Unfortunately, I can only find a small subset of these in the download
> folders for various OSs. At the moment I would need "g2gOverlap". Would
> anyone be able to tell me if it is possible to get a hold of these programs
> and if so where?
> 
> Thanks,
> 
> David