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
