Hi Peng, We recommend that you contact the lab that created the track that you are interested in for the specifics on how they calculated the signalValue. This information is located in the track description pages for each ENCODE track.
With regards to the mm9 table (wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdPk) located in the LICR TFBS track, we recommend that you contact the lab located on the track description page ( http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&c=chr1&g=wgEncodeLicrTfbs) to inquire about how they determined the peak coordinates. If you have further questions please provide specifics such as the genome, assembly, and the track that you are referring to so that we can better assist you. Thanks! Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Peng Yu <[email protected]> Date: Mon, Mar 19, 2012 at 9:01 PM Subject: Re: [Genome] The meaning of signalValue in ENCODE broadPeak format To: [email protected] On Mon, Mar 19, 2012 at 10:45 PM, Peng Yu <[email protected]> wrote: > Hi, > > It says "signalValue - Measurement of overall (usually, average) > enrichment for the region." on > > http://genome.ucsc.edu/FAQ/FAQformat.html#format13 > > But this does not describe how the number is calculated. Could anybody > let me know how it calculated? Thanks! It is also strange to me that chromEnd-chromStart is always 1000 (for example, in wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdPk). > with(data, table(chromEnd-chromStart)) 1000 23680 Should the binding region be a variable rather than a fixed number? -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
