Hello Craig, There are no chrom-specific wib files for this dataset.
One alternative is to use the public mySQL server instead. Follow the instructions here to get set up: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 If you do decide to create your own database, instructions are here: http://genome.ucsc.edu/admin/mirror.html Please let us know if we can help more, Jen UCSC Genome Browser Support On 7/10/10 7:16 AM, Benson, Craig C wrote: > > I am using hgWiggle without a database to pull phastCons scores for a given > chromosome position. It seems to be working pretty well using the following > two wib and wig files downloaded from here: > > ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/multiz46way/phastCons46way.wib > ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/phastCons46way.txt.gz > > ... using the set-up with the instructions from here: > http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database > > However, the only concern I have is that running hgWiggle without a database > with these two files is slow, which I suspect is from the size of the wib > file listed above and nearly 3 GB. I have noticed that there are *.wigFix > files for each chromosome listed here: > > ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/vertebrate/chr**.phastCons46way.wigFix.gz > > and so I was wondering... a) are there are associated *.wib files for these > individual chromosome files, b) is it possible to run hgWiggle using these > chromosome-specific *.wigFix files, and c) do you think it would be faster to > use the smaller, chromosome-specific files rather than the larger > phastCons46way files I am currently using? If not, I suspect using the > actual database with hgWiggle would be significantly faster, but I'm not > entirely excited or confident about trying to get a local copy of the > database up and running on my computer. Is there a set of instructions on > getting the database up and running locally? > > Thanks, > Craig > > Craig C. Benson, MD, MS > Med-Peds Resident, PGY-4 > University of Rochester Medical Center > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
