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
