Dear Amy, If you are just looking for the positions you will want to use the peaks table:
wgEncodeYaleChIPseqPeaksK562bYy1 and select the appropriate fields of interest using the table browser. To answer your questions: The signal value (in the peaks table) is calculated using the data value (from the signal table). To find out about the statistical significance of the additional fields, please see the description page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chrX&g=wgEncodeYaleChIPseq and within this page there is a links to more detail information: http://genome.ucsc.edu/goldenPath/help/qValue.html If you have further questions, please contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "meimeijo" <[email protected]> To: [email protected] Sent: Friday, December 17, 2010 2:09:12 AM GMT -08:00 US/Canada Pacific Subject: [Genome] How to get TFBSs from Yale TFBS data Dear Sir, I would like to know where the TF YY1 binds to chromosome X of human. I looked into the ChIP-seq data of Yale TFBS. There are mainly two formats there: peak and signal. TFBSs are known to be small regions of several bps. After I read the table schema, I still don't know how to get TFBSs via these data. I listed my problems as follows, and please give me some information if possible. 1) In signal data, there are four coulmns which are chr, chr start, chr end, and data value. What is the correlation between the "data value" and TFBSs? 2) In peak data, each item consists of the previous six columns of BED format with four additional columns. What is the correlation between these values with TFBSs? Really thanks for help. Amy Huang _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
