We do not keep sequence data in the database. The sequence is in the 2bit file. You will need to have the 2bit file available to extract sequence. The file is less than 1 Gb of data. Use the twoBitToFa program to solve all your problems. Please make sure your customers have a proper license to use the kent software.
--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 9:11:47 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. The reasons I was trying to use the sequenceForBed program are: - I did not want to download the huge volume of data from the UCSC web-site for such a small application - it is possible that users of my application will want to design primers for the human, rat, or mouse genomes - on any of the chromosomes. Besides there is the problem of keeping the data in sync with the UCSC site. - my input genomic region coordinates come in the form of a bed file. So the sequenceForBed program seems tailor-made for me if I can get it work directly on the UCSC mysql database. Would appreciate any further help you can give me. Kumar On 2/25/2011 8:56 PM, Hiram Clawson wrote: > 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
