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
