Hi Saubashya, We didn't receive the sample bed file attachments in your last email. Can you please send them to me directly?
Thanks! Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Saubashya Sur <[email protected]> Date: Thu, Nov 3, 2011 at 9:13 AM Subject: Re: [Genome] query To: Greg Roe <[email protected]> Cc: "[email protected]" <[email protected]> Hi, I am attaching two sample bed files of narrow peak regions for wgEncodeUwDGF one from hg 17 and the other hg 19 release. There are differences in the signal values and p values in both having same name. Conversion of hg 17 bed files to hg19 gives different coordinates. There are many files like this having similar names coming from different labs in ENCODE but with different releases. I need to know whether they are same or different. -Regards Saubashya Sur Department of Molecular Biology Umeå University, 90187 Umeå, Sweden ________________________________________ From: Greg Roe [[email protected]] Sent: Tuesday, October 25, 2011 12:33 AM To: Saubashya Sur Cc: [email protected] Subject: Re: [Genome] query 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
