[Genome] Genome masked?

[Galt Barber]

softmasked.  The .2bit structure internally
keeps a map of masked areas separate from
the actual 2bit data. (i.e. this is a list
or tree of ranges that are masked out),
but when gfServer is loading, it ignores
the softmasking that is there.

-Galt


On Thu, 24 Jan 2008, JIMMY LIN wrote:

> thanks for the answer. Is hg18.2bit masked (soft or hard)?
>
> ----- Original Message -----
> From: Galt Barber <galt at soe.ucsc.edu>
> Date: Thursday, January 24, 2008 2:10 pm
> Subject: Re: [Genome] Genome masked?
> To: JIMMY LIN <jimmy.lin at jhmi.edu>
> Cc: genome <genome at soe.ucsc.edu>
>
>
> >  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
> >  > _______________________________________________
> >  > Genome maillist  -  Genome at soe.ucsc.edu
> >  >
> >  >
>