Hi Qianqian, There are two sources of the data, which may be what is causing the mismatch. The data as displayed in the Browser has been compressed for display, as explained in the track methods.
Compressed data is what would be available from the Table browser or from the downloads server under "Annotation Database" (or an ftp to goldenPath/hg19/database/) The complete, uncompressed files are located at: http://hgdownload.cse.ucsc.edu/downloads.html#human Under "Multiple Alignments" (goldenPath/hg19/phyloP46way/) Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/26/10 9:38 PM, Qianqian Zhu wrote: > Hello, > > Could anyone please help me with some problems I had regarding to the > phyloP scores? > > I found there are some inconsistency between phyloP scores I download from > UCSC genome browser ftp site and the scores I got using Table Browser. For > example, the vertebrate phyloP score of position chr1:73942 (hg18) is -1.709 > from ftp site and is -1.71281 from Table Browser. Is something wrong here? > > Moreover, I don't understand what it means when the primate phyloP score > is identical to the vertebrate phyloP score but is different from the > placental mammal phyloP score at the same position. For example, at position > chr1:73942, the primate, placental mammal and vertebrate phyloP scores are > -1.709, -1.701, -1.709 respectively. These scores were obtained from genome > browser ftp site. When primate score and vertebrate score are identical at > the same position, I expect this means only alignments of primate species > are available at this position. If so, how could the placental mammal score > is different? > > I would really appreciate if anyone could help me out. > > Sincerely, > Qianqian > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
