[Genome] Are 11.ooc files for non-human genome assemblies available for downloading?

[Hiram Clawson]

Good Afternoon Junjun:

It only takes a few tens of seconds to generate an 11.ooc file:

blat myGenome.2bit /dev/null /dev/null -tileSize=11 -makeOoc=11.ooc -repMatch=300

We adjust the repMatch parameter based on the size of the genome.
A repMatch of 1024 is used for the human genome.  Adjust it
in terms of the relative size of the genome to the human size.
Smaller in proportion to how much smaller is your target genome,
or larger if your target genome is larger.

Blat will also calculate this internally each time you run it if
you do not supply it with one.

--Hiram

Junjun Zhang wrote:
> Hi UCSC folks,
> 
> Just a quick question: Are 11.ooc files for non-human genome assemblies
> available for downloading?
> 
> The 11.ooc file comes with BLAT is for the human genome. I need an 11.occ
> file for panTro2, I know BLAT can generate ooc files. But just wondering if
> UCSC has made the 11.occ files for all the assemblies before I do it myself.
> 
> Thanks,
> Junjun