thanks, Max! sorry.. yes, i'm on hg18. actually, a minute after I sent the question, i found out I could do this within the Table Browser if I only want to extract the maximum scores for all vertebrate conservation, by using the "summary statistics" - especially since I have a relatively short list of coordinates (~600). I still couldn't find the way to extract the scores out of certain files, though. The "summary statistics" wouldn't give the output for each coordinate range, but only for the entire file (which i thought was always the case, but turned out it's depending on the file I'm trying to extract.) I'm exploring it, and if I'm stuck, I'll post another question.
thanks a million! AW On Thu, Aug 12, 2010 at 2:59 PM, Maximilian Haussler <[email protected]>wrote: > Hi Agnes, > > if you're on a human genome, than I think galaxy has a function for > you that will immediately give you the data you need. Just upload your > regions, then use this function: > http://main.g2.bx.psu.edu/root?tool_id=aggregate_scores_in_intervals2 > > If you're on another genome, you would first need to get the > conservation score wiggle tracks from the Table Browser, check the > "send to Galaxy" option and then use this function with your regions. > > cheers > Max > > > > On Thu, Aug 12, 2010 at 1:33 PM, Agnes Williams > <[email protected]> wrote: > > Hi, > > I'm wondering if you could help me out with this. I have a list of ~600 > > coordinate ranges, and I would like to prioritize these regions based on > > conservation scores. Is there a way to do it so that the output file will > > only give me the maximum score for each coordinate range? I can go to > > "summary statistics" if I examine each region individually, but is there > a > > way to do this for a series of coordinate range? > > Also, if I have chosen the species to include in the conservation track > (so > > I'm not using the default setting), would the scores be calculated using > my > > sets of species or it will still be calculated using the default setting? > So > > would my output file from the Table Browser follow my setting or the > default > > setting? > > > > thanks a million in advance, > > AW > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
