Hi Gennady, When examining the 28-way conservation data in your file versus the browser display, remember that our datafiles have a zero-based start and a one-based end. That means you need to add "1" to the position base in this file to match it to the position in the browser display graph. The data you submitted and the track data are consistent when I view them. The blue line graphs positive conservation.
Also please be aware that we very recently updated our conservation track. When I open up both the old (now named 28-way Cons) and the new (named Conservation, which is 44-way), the result data is displayed differently and perhaps may be more clear. Default colors are blue = more conserved, red = less conserved. Check this out and let us know if this does not address your observations. For your reference, here is a link to our FAQ about the coordinate system we use: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 Jennifer Jackson UCSC Genome Bioinformatics Group Gennady Uho wrote: > Hi, > > I have a question about: > Vertebrate Multiz Alignment & PhastCons Conservation (28 Species) > > When I download datapoints for this track for the next coordinate I get: > track type=wiggle_0 name="28-Way Cons" description="Vertebrate Multiz > Alignment & PhastCons Conservation (28 Species)" > # output date: 2009-02-09 16:35:20 UTC > # chrom specified: chr5 > # position specified: 43326979-43326988 > # This data has been compressed with a minor loss in resolution. > # (Worst case: 0.0078125) The original source data > # (before querying and compression) is available at > # http://hgdownload.cse.ucsc.edu/downloads.html > variableStep chrom=chr5 span=1 > 43326979 1 > 43326980 1 > 43326981 1 > 43326982 1 > 43326983 0.992126 > 43326984 0.992126 > 43326985 0.858268 > 43326986 0.173228 > 43326987 0.165354 > 43326988 0.480315 > > When I watch exactly the same on genome browser it shows poor conservation > (blue graph) despite nucleotide conservation is almost perfect. Genome > version is hg18. > So I was wondering why the blue graph is not consistent with nucleotides data > and datapoints from the table. > > Thanks, > Gennady > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
