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
