[Genome] Settings for the simpleRepeat track

[Kayla Smith]

Hello Palle,

For the simpleRepeat track, the maxPeriod was bumped up from 500 to 2000 
in mid-2004. Our src/hg/trfBig/ program is what actually invokes TRF 
with the run parameters.  The invocation looks like this:

trf in.fa 2 7 7 80 10 50 2000 -m -d

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


Palle Villesen (BiRC) wrote:
> Hi,
> 
> I searched the archives and found an old mail from 2003 - but things tend to
> change over time.
> 
> Could someone please tell me which parameter settings were used for creating
> the simpleRepeat track in hg18 (using trf) ?
> 
> Thanks a lot,
> Palle Villesen
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