[Genome] elliotsEncode.mod for running phastCons

[Kate Rosenbloom]

Hello Jan,

The model files you've requested are now posted to the relevant  
phastCons
downloads areas on our test server and will soon be available on
our public download server.  For now, you can obtain them at:

http://genome-test.cse.ucsc.edu/goldenPath/hg18/phastCons17way/
http://genome-test.cse.ucsc.edu/goldenPath/dm3/phastCons15way/

For the hg18 conservation track, the following phastCons rate
parameters were used:

expected length      14
target coverage    .008
rho		                .28

The full set of command-line options  used are documented in the
doc/hg18.txt file.

     Cheers,
             Kate

On Feb 6, 2007, at 12:10 AM, Marek Szubert wrote:

> Hi
>
> I would like to run phastCons on a subset of the hg18 multiz17way  
> multiple
> sequence alignments that I have FTPed and  wondered if you could send  
> me the
> contents of the phyloHMM  model file :
>
> /cluster/store5/gs.18/build35/bed/multiz17way.2005-12-20/cons/ 
> elliotsEnco
> de.mod
>
> that is used later in running phastCons to produce the conservation  
> scores
> (named in /kent/src/hg/makeDb/doc/hg18.txt ). It would be good for me  
> to see
> the phylogenetic tree used and what phastCons rate parameters were  
> used as a
> basis for my own runs.
>
> If possible I would also like to request the two equivalent noncons  
> and cons
> files for the dm3 multiz15way  model files :
> /cluster/data/dm3/bed/multiz15way/phastCons/run.estimate/ 
> ave.noncons.mod
> and    ave.cons.mod
>
> Thank you for your help
>
> Jan Szubert, University of Queensland.
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