Hello Mohsen, The table you referenced does not contain data for every base. Rather, it contains pointers into a binary ".wib" file that contains the data. More information on wiggle tracks and wiggle data is here:
http://genomewiki.ucsc.edu/index.php/Wiggle http://genome.ucsc.edu/goldenPath/help/wiggle.html Direct download of the data you are interested in is available from our downloads page, here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/ I hope this is helpful. -- Brooke Rhead UCSC Genome Bioinformatics Group On 06/04/09 07:30, Mohsen Khorshid wrote: > Dear Sir/Madam, > > I have a long list of Genomic Loci. I would like to calculate the > PhastCon scores over these region. I would like to calculate the > basewise scores by accessing the PhastCon Bin scores using the mySQL > direct access but I have a problem with data retrieval. > > Lets us assume the locus is located at : > chr12:56439310-56439395 > > I assume I need to query the "phyloP44wayPlacMammal" using the following > query: > select * from phyloP44wayPlacMammal where chrom="chr12" and > chromStart>=56439310 and chromEnd <=56439395; > > > But most of the time I get empty entries back. So then I can not go > basewise and calculate the phastCon over the bin(s). > > Could you please let me know if I am making mistake somewhere? > > > Cheers, > Mohsen Khorshid > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
