Hello, Li. First, allow me to point out the fact that two different labs are naturally going to use slightly different methods and algorithms in obtaining their data, so it is not unusual to see the types of differences that you saw. Visually, the data is very similar. For a deeper explanation of the methods used to generate the data, I encourage you to read the Display Conventions and Configuration and the Methods sections of the respective tracks:
Duke: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase UW: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwDnase As far as replicates, some labs release pooled replicate data while others release only the individual replicates. While clearly not identical, the replicates are generally very similar to each other and both the pooled and individual replicate data sets are available for download. If you require more specific information than what is contained on the description pages, the Credits sections list the contact information of the labs that created the tracks. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of ??? Sent: Monday, June 18, 2012 6:34 PM To: [email protected] Subject: [Genome] ENCODE Histone Modifications Dear Professor: I am new in studying histone modifications. I saw that there are DNaseI HS data from duke and UW. I just have two questions, one is rep1 and rep2 data, should I combine them when I use it or else? second, I found that DHS data between two university are different, I think the difference is a bit large, I do not have experience in DHS-seq, is it normal that the difference is big? Looking forward to your reply. Thanks. Li Yuanfeng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
