Hi Hiram! Thanks for your prompt response. When I tried the 3-line .hg.conf file that you suggested, the sequenceForBed program failed immediately with the message:
Can't find profile central in hg.conf Would appreciate any more help you can give me. Thanks! Kumar On 2/25/2011 10:45 AM, Hiram Clawson wrote: > Good Morning: > > You can avoid all of this trouble by downloading the .2bit sequence file, > for example: > > ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit > > And then use the twoBitToFa program to extract sequence from this > file with locations specified in a file. This type of sequence > extraction > needs no access to the database. > > If other functions of your procedure need database access, you can use > the simple .hg.conf file with three lines as indicated: > > db.host=genome-mysql.cse.ucsc.edu > db.user=genomep > db.password=password > > You do not need all of the other .hg.conf parameters to use the > public mysql server. that other business is for running a local > copy of the genome browser. > > I hope this information is helpful. Please feel free to contact the > genome mail list (one list only please) again if you require > further assistance. > > --Hiram > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
