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 >> >> -- Thong Nguyen School of Mathematics, Statistics and Applied Mathematics NUI Galway, Ireland _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
