Hi Saubashya, Please see this information on downloading from our site via ftp: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download
Example Encode dir: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/ Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 10/24/11 1:16 AM, Saubashya Sur wrote: > Hi, > > We are interested in downloading the defined peaks (narrow peaks or high > confidence peaks) for all factors mapped using ChIP-chip or ChIP-seq by the > ENCODE consortium. We have been unable to find a way to do this in a simple > way without searching for each individual factor and then manually download > each of them. Any recommendation on how to do this would be appreciated. > > -Regards > > Saubashya Sur > Department of Molecular Biology > Umeå University, 90187 > Umeå, Sweden > ________________________________ > From: Vanessa Kirkup Swing [[email protected]] > Sent: Thursday, October 20, 2011 6:37 PM > To: Saubashya Sur > Cc: [email protected] > Subject: Re: [Genome] query > > Hi Saubasha, > > It appears that you are downloading data from the UW Histone track on hg18. > I'm going to assume that you are referring to the fourth column of your > bedGraph column with regards to ratios. Here is information about the > bedGraph format: > > http://genome.ucsc.edu/goldenPath/help/bedgraph.html > > The forth column is a dataValue. > > Information about the data for the track can be found on the description > page: > > http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chrX&g=wgEncodeUwChIPSeq > > If the description page doesn't answer your question about the data, then you > will need to contact the lab that provided the data. This information can be > found under the "Credits" section. > > We hope this helps you. If you have further questions, please contact us at: > [email protected]<mailto:[email protected]>. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > > > ---------- Forwarded message ---------- > From: Saubashya > Sur<[email protected]<mailto:[email protected]>> > Date: Wed, Oct 19, 2011 at 7:00 AM > Subject: [Genome] query > To: > "[email protected]<mailto:[email protected]>"<[email protected]<mailto:[email protected]>> > > > Hi, > I was looking at the ENCODE datasets of human for CTCF. I am attaching 4 > screenshots with this email. In the first screenshot i have downloaded the > bigwig files i highlighted. I converted them to bedgraph format which you can > visualise in the other three screenshots. I wanted to know whether they are > the ratios or not. If you could provide me details of the files it would be > fine. > -Regards > > Saubashya Sur > Department of Molecular Biology > Umeå University, 90187 > Umeå, Sweden > > _______________________________________________ > Genome maillist - [email protected]<mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
