Hi Emma, 1) The range was chosen based upon the data to maximize the signal for all bases that have strong evidence of the histone mark. The biological signal itself can be skewed for many reasons. If there is a single datapoint the is off the charts, then it might have a signal of 10000 and force all others to something much lower. That one data point should not hide the rest of the signal.
For a precise explanation of how the the signal was calculated, you'll want to contact the lab in question. 2) Locate the wgEncodeBroadHistone peak table in the table browser and click the "describe schema" button next to the table name. It will show all the fields in the table and define each of them. You'll also find additional information in the track's description in the genome browser (e.g. http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chrX&g=wgEncodeBroadChipSeq) Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 9/19/11 10:16 AM, Emmanouela Repapi wrote: > Hello, > > I have two questions regarding the histone modification markers tracks > (ENCODE Regulation Super-tracks). > 1) How were the default ranges for the tracks set? i.e. why are the default > ranges for H3K4Me1 from 0 to 50, and for H3K4Me3 from 0 to 150? Do these > depend on the markers or the regions? I am trying to visualise the signal > enrichment but I am not sure which ranges would be more appropriate in order > to distinguish signal from noise. > 2) I have downloaded the files wgEncodeBroadHistone (broadPeak files) from > the ucsc downloads and I want to create a binary score for each region - > signal enrichment/non enrichment. What are the "signalValue", "pValue", > "qValue", of these files? > Any help/references would be much appreciated! > > Thanks, > Emma > > > > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
