Here is one approach that has worked for me: download it as a wig file
convert to bigWig format using wigToBigWig (c.f. http://genomewiki.ucsc.edu/index.php/Kent_source_utilities and/or http://hgdownload.cse.ucsc.edu/admin/exe/) extract regions of interest from the bigWig version using bigWigSummary if you're doing analysis in R, then the following function might help bigWigSummaryScore = function(path,chr,start,end) { ## PURPOSE: proviude fast indexed retrieval of vector of scores from bigWig ## file <path> (such as may be used to store phastCons scores). start and ## end are 1-based (comporting with GRanges) ## ## Implemented as wrapper of Jim Kent's bigWigSummary. Special care ## is taken to return NA for all ranges lacking data (as is NOT done ## by the command line tool). ## ## "when you're giving bigWigSummary coordinate input on the command ## line, it's expecting it in our bed format, which is zero based." ## per: ## https://lists.soe.ucsc.edu/pipermail/genome/2011-February/025099.html ## call <- sprintf('bigWigSummary %s %s %s %s %s',path,chr,start-1,end,end-start+1); result=suppressWarnings( ## thus supressing, eg, "no data in region chrU:10047341-10047388 in dm3_phastCons15way.bw" lapply(strsplit(system(call, intern=TRUE, ignore.stdout=FALSE, ignore.stderr=TRUE)[1], "\t"),as.numeric)[[1]]) if(length(result)==1 && is.na(result[[1]])) { result=rep(NA,end-start+1) } result; ~Malcolm > -----Original Message----- > From: [email protected] [mailto:genome- > [email protected]] On Behalf Of PKDK > Sent: Friday, May 20, 2011 3:15 PM > To: [email protected] > Subject: [Genome] question about phyoP conservation data > > Hello > > I need to find a way to extract the phyloP conservation data for > specific areas of the chromosome. I have over 3000 specific areas that > I need to look at and extract the phyloP values for them. I thought > that I could just download the mass data file but it seems like the > file does not take into account gaps or areas on the chromosome where > the phyloP data is not given. > > For example if I wanted the following phyloP for the query : > chr1:1220332130-1220332150 > > On the large phyloP file the data for chr1, it starts at 10918. If > there are any gaps between 10918 and 1220332130, then the index to the > nucleotide number will be thrown off. Is there any way to compensate > for gaps? > > Or is there a better way to extract phyloP data? > > Thanks in advance > > Dave > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
