Good Morning Alex: The values you get from the FTP download files are the original "correct" values.
The values obtained from the table-browser are, as indicated, compressed values that have a loss in resolution from the original "correct" values. They are perfectly good for the purpose of making the graph on the genome-browser. See also: http://genomewiki.ucsc.edu/index.php/Wiggle noting the "Known Issues" section. --Hiram Alexander Donath wrote: > Hi, > > I stumbled across an issue which was already mentioned in the mailing list a > few > years ago and seemed to be solved. > I've downloaded phastCons values for the multiple alignments of the > chromosomes > of the 6 nematodes via the browser tool and the ftp server > (http://hgdownload.cse.ucsc.edu/goldenPath/ce6/phastCons6way/). Somehow the > values for the positions differ, e.g.: > > values from the table tool: > > track type=wiggle_0 name="Conservation" description="Multiz Alignment & > Conservation (6 nematodes)" > # output date: 2008-11-12 16:34:21 UTC > # chrom specified: chrI > # position specified: 1-10000000 > # 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=chrI span=1 > 1521 0.208543 > 1522 0.339598 > 1523 0.415472 > 1524 0.601709 > 1525 0.718969 > 1526 0.787945 > 1527 0.822433 > 1528 0.829331 > 1529 0.822433 > 1530 0.787945 > > values from the chrI.data.gz file from the ftp directory: > > fixedStep chrom=chrI start=1521 step=1 > 0.215 > 0.345 > 0.419 > 0.604 > 0.720 > 0.793 > 0.823 > 0.833 > 0.827 > 0.789 > > > How is that possible? And which values are correct? > > Best, > Alex > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
