Dear list,
The blatSuite.zip file (downloaded from
http://genome-test.cse.ucsc.edu/~kent/exe/linux/) comes with a 11.ooc
file. I couldn't find any information regarding which genome was used to
generate this file. Richard asked a similar question here
https://lists.soe.ucsc.edu/pipermail/genome/2004-February/003964.html:
1) What's the difference going to between genome versions?
Is it worth re-creating a new version or will the ooc file
produce similar results?
2) Does it make sense to run the ooc file for the human on
the mouse genome?
Additionally on the FAQ (http://genome.ucsc.edu/FAQ/FAQblat.html#blat6),
it was mentioned that "The 11.ooc file contains sequences determined to be
over-represented in the genome sequence."
So it was a bit confusing to me; do all genomes have these
over-represented sequences, hence the default 11.ooc file that comes with
the blatSuite.zip? Or I should generate my own ooc file as has been
pointed out in previous emails from this mailing list?
Thank you very much for you help.
Best,
Dave
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