You do not need to use the sequenceForBed program Please use the twoBitToFa program as I mentioned earlier.
--Hiram ----- Original Message ----- From: "B.Kumar" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected], "B.Kumar" <[email protected]> Sent: Friday, February 25, 2011 8:16:48 PM Subject: Re: Cannot access cart tables in central (nor backupcentral) database. Please check central and backupcentral settings in the hg.conf file and the databases they specify. 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
