Hi Dina,
Cat files into one and convert into bigWig. UCSC has a tool
"wigToBigWig" on this same downloads area available (see section "Source").
Or, in this case, you can grab our version of the data via rsync. We
have the file for hg18 and for hg19 - I should have mentioned this
originally! If you get the hg19 genome, the data will be in the "misc"
directory, and the location dir has the .loc file with an entry you can
model after (but you will need to of course alter the path to match your
own system's data path):
http://wiki.galaxyproject.org/Admin/Data Integration
Hopefully this helps,
Jen
Galaxy team
On 2/1/13 11:35 PM, Dinanath Sulakhe wrote:
Hi Jen,
Thanks for your reply.
I looked at these phyloP46way-Primates datasets here :
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/primates/
They don't seem to be in bigwig format and also there is one file per
chromosome. The PhyloP's add_scores.loc instructions give an impression that it
may take just one bigwig file. If this is the right data, do i need to convert
them into bigwig format and how? And how to configure add_scores.loc to provide
multiple files (per chromosome)?
Thanks,
-Dina
On Feb 1, 2013, at 11:55 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:
Hi Dina,
These data are available from USCS in their downloads area at
http://genome.ucsc.edu. See the left side bar for the 'Downloads' link, then
navigate to the genome release and track files (are clearly labeled).
Best,
Jen
Galaxy team
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
On Feb 1, 2013, at 9:45 PM, Dinanath Sulakhe <sula...@mcs.anl.gov> wrote:
I am trying to setup PhyloP in galaxy. In the add_scores.loc file it says we
need the phyloP46way.primate.bw (BigWig) file.
#hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw
Is there a downloadable bigwig files somewhere for hg19 that I can use?
From the instructions on bigwig, it looks like we have to create a bigwig file
from the wig files.
Thanks, -Dina
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Galaxy Support and Training
http://galaxyproject.org
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