Hello Illes, The first recommendation is to use the most recent version of the PhyloP data - contained in both hg18 and hg19 under the composite track heading "Conservation". In hg18, this includes 44 species and in hg19 46 species.
Instructions for rsync or ftp are in the README files along with the data at these locations: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way/ http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/ Please note that scores are pre-computed based on logical species groupings. In this case, placentalMammals, primates, and vertebrates (with some special subsets of these group for chromX in hg19). If you want to generate score for pairwise or other groupings, please see the track description's Methods about the PHAST package (http://compgen.bscb.cornell.edu/phast/). The general idea would be to use the (filtered) MAF data as input and generate the scores yourself. If you need any help with kent source tree utilities please let us know, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Illes Farkas" <[email protected]> wrote: > From: "Illes Farkas" <[email protected]> > To: [email protected] > Sent: Tuesday, January 19, 2010 6:15:26 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] ? download PhyloP track with settings > > Thanks to all for running the services at the UCSC Genome Browser. > > I'd like to download the track "vertebrate basewise conservation by > PhyloP" > for ~1000 regions (100-500bp each) in human. Before downloading this > track > can I change the "28-Way Cons Track Settings" at > http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=multiz28way? > > For a wet lab application I'd like to see the basewise (or 5-10bp > window-wise) conservation scores of these human genomic regions with > conservation in (a) only human+mouse or (b) only vertebrates (c) etc. > Is it > possible to do this with perl+wget with requests like > http://server.ucsc.edu/script.cgi?par1=one&par2=two&;... and then > processing > the output (with perl)? > > Thanks, > Illes > -- > http://hal.elte.hu/fij > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
