Hello Zhang, To obtain the actual data values, use output format = data points (instead of BED, which only provides positional information).
The new output will be in compressed wiggle format. A description of that format is here: http://genome.ucsc.edu/goldenPath/help/wiggle.html And if you would like the complete data per base (instead of the compressed summary), the files can be anonymously ftp'd from the downloads server here: http://hgdownload.cse.ucsc.edu/downloads.html#human scroll to the build (hg19, hg18, etc.) and look for the heading "Multiple Alignments" and the sub-link "Basewise conservation scores (phyloP) of 45 vertebrate genomes with Human" For hg19, this would be: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way/ A description of the files and ftp/rsync help is in the README To directly answer your question, no the data is not a complete 1-1 exact match, these are probability scores. The Conservation track has help describing the process in the Methods section (click on the track name in the main Assembly viewer). Hopefully this helps. Please feel free to contact the mailing list support team again if you would like more assistance. Warm regards, Jen UCSC Genome Browser Support On 9/1/10 9:18 AM, Zhang Wensheng wrote: > Hello, > > I am a new UCSC Genome Browser user. I have a question about table "Mammal > Cons(PhyloP44wayPlacMammal" in clad:Mammal and genome:Human. When the position > information was specified via "define regions", > > > chr1 869396 869824 > chr1 869445 869936 > chr1 890434 890958 > chr1 899818 900345 > chr1 924205 924301 > > I got the the output file in BED format as following, > > track type=wiggle_0 name="tb_phyloP44wayPlacMammal" description="table browser > query on phyloP44wayPlacMammal" visibility=2 url= > > chr1 869396 869824 chr1.1 > chr1 869445 869936 chr1.1 > chr1 890434 890958 chr1.1 > chr1 899818 900345 chr1.1 > chr1 924205 924301 chr1.1 > > > Could please help me by explaining this result? Specially, I want to know if > it > means that, in the case of the first line, the sequence Human ch1:86939-869824 > can be perfectly aligned with a region of other genomes (one or all). > > > Thanks you very much > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
