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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
