Hi Thong, Unfortunately, each Histone modification and Chip-Seq track is done slightly differently depending on the lab. We advise looking at the track descriptions for analysis details. If you have further questions contact the person that is flagged as Contact for that Encode Data.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 11/23/10 10:18 AM, NGUYEN Trung Thong wrote: > Dear Brooke, > > Thanks a lot for this help. I would like to use the ENCODE histone > modifications data and apply your peak calling method for my ChIP-seq data. > I therefore would like to understand well your method and wish you help me > out with some questions below: > > - How did you normalize data from pooled replicates? > - Did you combine Input Control with ChIP-seq data to find peaks? If so, how > did you do that? > > Thanks again for your help! > > Thong > > On Mon, Nov 8, 2010 at 9:36 PM, Brooke Rhead<[email protected]> wrote: > > >> Hi Thong, >> >> These are genome-wide data. In general, unless an ENCODE track is listed >> under one of the "Pilot ENCODE" headers on the main Genome Browser page ( >> http://genome.ucsc.edu/cgi-bin/hgTracks), it is genome-wide data. Another >> way to double-check that any particular track you are using is genome-wide >> is to hit the "schema" link/button on the track details page or in the Table >> Browser. If the table name starts with "wgEncode" it is genome-wide ("wg" >> stands for "whole genome"). >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 11/07/10 17:25, NGUYEN Trung Thong wrote: >> >> >>> Dear friends, >>> >>> I am interested in histone modifications ChIP-seq data and have found two >>> sources (by Broad Institute and by Univ. Washington) available on the UCSC >>> Genome Browser. If you don't mind, could let me know whether these are >>> genome-wide data or just some parts of the human genome? I am using >>> genome-wide histone modifications data of Barski et al. (Cell 2007) and >>> hope >>> to have more data from different cell lines. >>> >>> Thanks a lot, >>> >>> Thong >>> >>> >>> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
