Thanks Roe! This helped! Alberto On 14/06/2012 17:52, Greg Roe wrote: > Hi Alberto, > > The table you're looking at has some data to help display the track > when users are zoomed out, which isn't all that useful to look at. I > think what you're wanting can be found on the description page for > that track > (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way). Scroll > down (about half-way) to where it says, "Downloads for data in this > track are available:". I think you'll find the files you want there. > > If you have any additional questions, please reply to: > [email protected] > - > Greg Roe > UCSC Genome Bioinformatics Group > > On 6/4/12 7:06 AM, Alberto de la Fuente wrote: >> Hello, >> >> For both PhyloP and PhyloCons the tables have the same format. What I >> understand is that conservation for elements of 1024 bases is provided. >> What I am not sure of is what"sumData" provides. This smaller this >> number, the more conserved the element is? I don't see any explanation >> on the Genome Browser website :( >> >> Where can I download the actual scores which PhastCons and PhyloP >> provided? >> >> Thanks, >> >> Alberto >> >> >> On 04/06/2012 13:16, Adam Siepel wrote: >>> Hi Alberto -- good to hear from you! I hope all is well. >>> Your question is about the "wiggle" tracks in the browser more than >>> about phyloP and phastCons, and would probably be better addressed to >>> the browser staff. But I believe sumData is just the sum of the >>> basewise scores in a 1Kb block, and is only used to expedite bulk >>> statistical calculations. It's not generated or used by the >>> conservation programs. The scores themselves are stored in a >>> separate, binary file known as a "wib" file. These can be downloaded >>> from UCSC in binary or text form. >>> Adam >>> >>> On Jun 4, 2012, at 4:44 AM, Alberto de la Fuente wrote: >>> >>>> Dear Adam, >>>> >>>> >>>> I have a question about the tables you provided to the Genome browser. >>>> For both PhyloP and PhyloCons the tables have the following format. >>>> What I understand is that conservation for elements of 1024 bases is >>>> provided. What I am not sure of is what"sumData" provides. This >>>> smaller this number, the more conserved the element is? I don't see >>>> any explanation on the Genome Browser website :( >>>> >>>> Thanks, >>>> >>>> Alberto >>>> >>>> field example SQL type description >>>> bin 585 smallint(5) unsigned Indexing field to speed >>>> chromosome >>>> range queries. >>>> chrom chr1 varchar(255) Reference sequence chromosome >>>> or scaffold >>>> chromStart 10917 int(10) unsigned Start position in >>>> chromosome >>>> chromEnd 11941 int(10) unsigned End position in chromosome >>>> name chr1.0 varchar(255) Name of item >>>> span 1 int(10) unsigned each value spans this many bases >>>> count 1024 int(10) unsigned number of values in this block >>>> offset 0 int(10) unsigned offset in File to fetch data >>>> file /gbdb/hg19/multiz46way/phas... varchar(255) path name >>>> to data >>>> file, one byte per value >>>> lowerLimit 0.002 double lowest data value in this block >>>> dataRange 0.34 double lowerLimit + dataRange = upperLimit >>>> validCount 1024 int(10) unsigned number of valid data >>>> values in >>>> this block >>>> sumData 126.353 double sum of the data points, for >>>> average and >>>> stddev calc >>>> sumSquares 26.4071 double sum of data points squared, >>>> for stddev calc >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> Alberto de la Fuente >>>> Senior Researcher >>>> CRS4 Bioinformatica >>>> http://www.bioinformatica.crs4.it/ >>>> http://biowiki.crs4.it/biowiki/AlbertodelaFuente >>>> CRS4 Bioinformatica c/o Parco Tecnologico della Sardegna >>>> Edificio 3 Loc. Piscina Manna >>>> 09010 PULA (CA) ITALY >>>> Tel: +39 070 9250 433 >>>> Fax: +39 070 9243 3200
-- Alberto de la Fuente Senior Researcher CRS4 Bioinformatica http://www.bioinformatica.crs4.it/ http://biowiki.crs4.it/biowiki/AlbertodelaFuente CRS4 Bioinformatica c/o Parco Tecnologico della Sardegna Edificio 3 Loc. Piscina Manna 09010 PULA (CA) ITALY Tel: +39 070 9250 433 Fax: +39 070 9243 3200 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
