Hi David,

Apologies for the late reply, but were trying to get you a complete answer, but it is not ready. Meanwhile, perhaps this will help.

So, for phastCons:

Needs to be converted to binned array files using wiggle_to_binned_array.py from bx-python.

The loc file points to a base directory containing the binned array files split by chromosome.

The phastOdds are different, requiring a special output format. Right now we are not sure if it is still supported.

James or another team member will follow up. If you have figured it out yourself, please post back to the list (if you have time) so that we and the list members can learn.

Thanks again!


Galaxy team

On 2/1/11 6:58 AM, David Hoover wrote:
Does anyone have a clear explanation of what files are required/available for Get 
Genomic Scores ->  Aggregate datapoints, Compute phastOdds (binned_scores.loc 
and phastOdds.loc files)?  I know there are .mod and .pp files and .wigFix files 
from UCSC, but I can't figure out exactly what Galaxy is looking for.  Do I need 
to install PHAST and generate these score files?

David Hoover
Helix Systems Staff
galaxy-dev mailing list

Jennifer Jackson
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