Hello, We wanted to follow up and send you a path to the instructions in the kent source tree at: src/product/README.*
A short description for many of the utilities (including hgWiggle) is here: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jacob Biesinger" <[email protected]> wrote: > From: "Jacob Biesinger" <[email protected]> > To: [email protected] > Cc: [email protected] > Sent: Monday, August 31, 2009 11:40:29 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] PhastCons scores programmatically? > > Sorry-- I'm not sure where the hgWiggle program is. I have the CVS > repository but I don't see it under src/hg I only see wiki pages > describing > downloading the repo, not building or using specific tools. Where is > the > manual for all this stuff? > > -- > Jake Biesinger > > > > On Mon, Aug 31, 2009 at 8:07 AM, Jacob Biesinger > <[email protected]>wrote: > > > > > > > Begin forwarded message: > > > > *From: *Hiram Clawson <[email protected]> > > *Date: *August 30, 2009 8:27:01 PM PDT > > *To: *Jacob Biesinger <[email protected]> > > *Cc: *[email protected] > > *Subject: **Re: [Genome] PhastCons scores programmatically?* > > > > Good Evening Jacob: > > > > The kent source tree command: hgWiggle can be used to > > fetch regions from these files. See also: > > > > > http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database > > > > The actual original scores can be found in the files: > > ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/ > > > > but there is no real access method to those file, they are simple > > ASCII files which you would have to read and parse in order to > > get the scores out of them. You might be able to convert them > > to bigWig files and use the access program for those files. > > See also: > > ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/linux.x86_64/ > > > > --Hiram > > > > Jacob Biesinger wrote: > > > > Hi! > > > > Interested in getting the PhastCons score for a few thousand regions > in > > Drosophila melanogaster. I could use galaxy, but I'd rather have > > programmatic access to the data (there's no command line interface > in > > Galaxy, unfortunately!) > > > > The public mysql server is set up to only give me the offsets in > the > > appropriate phastCons score files. Is there any way to get those > scores > > programmatically short of pulling those files down, getting the > offset etc > > etc? > > > > Thanks! > > > > -- > > > > Jake Biesinger > > > > _______________________________________________ > > > > 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
