Good Morning Tony: You are on the right track for this. You will have to use hgWiggle individually on each region.
If you are using it with the database connection option: "Using the UCSC public MySQL server" http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database#Using_the_UCSC_public_MySQL_server hgWiggle will run rapidly and a loop to run several thousand items shouldn't take very long. Beware of the type of wiggle data you are working with. Some types of data lose their real meaning if they are put together in an average. For example phastCons and phyloP data: https://lists.soe.ucsc.edu/pipermail/genome/2005-October/008744.html and follow up information: https://lists.soe.ucsc.edu/pipermail/genome/2005-October/008748.html --Hiram Tony Capra wrote: > Hello, > > I would like to get the average of some wiggle format data over > windows of a genome. I could get the what I need by several thousand > runs of hgWiggle using -doStats and the -position flag to specify each > region of interest in turn. Is there a way to get hgWiggle to produce > its -doStats output put for a set of input regions with a single > call? When I use the -bedFile option, it summarizes the scores over > all the regions in the bed file, not each one individually. > Alternatively, is there a different program I should use or a > different way to think about doing this? > > Thanks, > Tony _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
