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
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 <sulakhe@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 ___________________________________________________________ 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:
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 <jen@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 <sulakhe@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 ___________________________________________________________ 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:
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 <jen@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 <sulakhe@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 ___________________________________________________________ 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:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
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Jennifer Jackson