Dear Mary, The hg18 "uwNucOccA375.txt" file seems to have split the DNA sequences into blocks of 1024 bp. Is there a simple way to see whether a block is of frequent nucleosome occupancy or not? Another question: Although the field "lowerLimit" is explained in the schema as "lowest data value in this block", I am not sure what that means.
Thank you for your help! Regards, Hao ----- Original Message ----- From: "Mary Goldman" <[email protected]> To: "Hao Zheng" <[email protected]> Cc: [email protected] Sent: Tuesday, September 21, 2010 6:22:16 PM GMT -05:00 US/Canada Eastern Subject: Re: human genome (hg18) nucleosome position Hi Hao, In order to get the SVM score for each 50-mer, you will need the .wib file that the table uwNucOccA375 is referencing. This file can be found here: ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/wib/uwNucOccA375.wib. More information about how to use this file can be found here: https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013503.html. I hope this information is helpful. Please do feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 9/21/10 1:44 PM, Zheng, Hao wrote: > 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
