Hello Hao, You may find one of our utilities, hgWiggle, useful for extracting the scores and generating statistical summary data from the wib file. You can find instructions about downloading and installing kent source utilities here:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads http://genome.ucsc.edu/admin/jk-install.html With the actual source download residing here: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip You can instructions for using hgWiggle here: http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database Regarding your question about "A375" it is a cell line as described on the description page for the Nucleosome Occupancy track here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chr9&g=uwNucOcc&g=uwNucOcc For more information about how A375 was used etc. please see the original reference cited at the bottom of that page: Ozsolak F, Song JS, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol. 2007 Feb;25(2):244-8. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 9/22/10 9:03 AM, Zheng, Hao wrote: > Dear Colleague, > > I've read through the url you provided: > https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013503.html > and the urls within. > > I am still not clear how to extract the score from uwNucOccA375.wib. > I need the scores for whole genomes, not small regions of the genome. > > Please let me know whether you have further suggestions. > > > Best, > 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 >>>> >>>> >>>> >>>> >>> >>> >> >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
