[Genome] Genome masked?

[Galt Barber]

For our dna gfServer there is no explicit masking used at all.
However, over-used tiles will not be able to participate
in triggering an alignment candidate.  With gfServer,
this number can be increased by setting -repMatch.
However doing so might lead to an explosion of
junk that needs to be filtered out, and may make
BLAT runs slower.

See our BLAT FAQ.

-Galt


On Thu, 24 Jan 2008, JIMMY LIN wrote:

> Hi:
>
> With the default options with gfServer and hg18.2bit, is the genome
> masked for repeats? Which staged does the genome masking occur (i.e.
> before generation of 2bit, loading genome into memory with gfserver,
> when queried with gfclient)?
>
> Thanks,
> Jimmy
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