Dear Colleague, I've downloaded the hg18 file "uwNucOccA375.txt".
In the table schema, it is said that "The output of the SVM is a unitless discriminant score. In the browser, the score of a 50-mer is assigned to its 26th base. Canonically, a score of 0 indicates an uncertain assignment; a score of 1.0 corresponds to a confident prediction for being in the positive class (i.e., a position of frequent nucleosome occupancy), and a score of -1.0 corresponds to a confident prediction for being in the negative class." I want to decide whether a segment of hg18 DNA is of frequent nucleosome occupancy or nucleosome-free. I didn't figure out how to get the score from the "uwNucOccA375.txt" file. Is there a column in the "uwNucOccA375.txt" file correspond to the score (output of the SVM)? Do you have any suggestions? Thanks, Hao > ----- Original Message ----- > From: "Mary Goldman"<[email protected]> > To: "Hao Zheng"<[email protected]> > Cc: "genome"<[email protected]> > Sent: Tuesday, September 21, 2010 3:24:26 PM GMT -05:00 US/Canada Eastern > Subject: Re: [Genome] human genome (hg18) nucleosome position > > Hi Zheng, > > I recommend our Nucleosome Occupancy track on hg18: > http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=uwNucOcc. > > I hope this information is helpful. Please feel free to contact the > mail list again if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > On 9/21/10 7:47 AM, Zheng, Hao wrote: > >> Dear Colleague, >> >> >> >> Does UCSC has any record for the nucleosome position of human genome (hg18)? >> >> Thanks, >> >> Hao Zheng >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > -- ################################################################ Hao Zheng PhD Candidate----Bioinformatics and Digital Signal Processing Georgia Institute of Technology 210 Technology Circle Savannah, GA 31407 Phone: 404-543-2836 Web: http://users.ece.gatech.edu/~hzheng7/ ################################################################# _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
