Hello, We noticed that the data point is actually set to be between bases. Perhaps you need to make a correction in the coordinates so that the base with the SNP is specified? Right now the start and stop are the same value - the need to be one different to represent a single base.
Some coordinate help: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms bedGraph format help: http://genome.ucsc.edu/goldenPath/help/bedgraph.html Another format that may be interesting to try is bigWig: http://genome.ucsc.edu/FAQ/FAQformat#format6.1 http://genome.ucsc.edu/goldenPath/help/bigWig.html If you would recreate the data so that the datapoints are per base, we can start a review process. Thank you, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Roberto Amato" <[email protected]> wrote: > From: "Roberto Amato" <[email protected]> > To: [email protected] > Sent: Monday, November 30, 2009 9:32:03 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] high density FST track > > Greetings, > we produced a track for Genome Browser that perhaps can be of any > interest to other peoples. We computed the fixation index (FST) on > the > most up to date dataset available from HapMap. > In particular, we computed the difference in the allelic frequencies > of 3 populations, broadly reflecting a continental subdivision, by > means of the Weir&Cockerham FST estimator. Data are from the last > HapMap release (HapMap Public Release #27 merged II+III) and regards > about 3.3 millions of SNPs. The detailed description of materials and > methods can be found in the paper "Genome-Wide Scan for Signatures of > Human Population Differentiation and Their Relationship with Natural > Selection, Functional Pathways and Diseases" (PLoS ONE 4(11): e7927. > doi:10.1371/journal.pone.0007927) available at the URL > http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007927 > It is worth stressing that, in our opinion, the problem is of quite > general interest. For example, we received many requests for the > script we developed to compute the FST at a genome-wide level. > We know that another track regarding FST is already present in the > browser but some important differences exists. The most important > ones > are that HapMap data are very dense and also concerns X, Y and > mitochondrial chromosomes. Moreover, the signal is base-wise and not > smoothed, thus the actual value of selective pressure for each SNP is > available (this can be of particular interest, for example, to those > working on GWAS). > The track is available at the URL > > http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr17&hgt.customText=http://www.geneticamedica.unina.it/FstTrack.bed.bz2 > > Track is BedGraph format and concerns hg18 database. If it can be of > any relevance for you, all data (including heterozigosity and many > other measures) are also stored in a local MySQL database. > We will be pleased if you can consider to distribute this data by > means of your browser. > Looking forward for to hearing from you. > Regards, > Roberto Amato > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
