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.
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?
Helix Systems Staff
galaxy-dev mailing list
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: