Hi Hiram! You were right! It was very straightforward to download the 2bit file and to use twoBitToFa to create a fast file of sequences given a bed file of regions. Thanks very much for your help! Kumar
On 2/25/2011 11:21 PM, Hiram Clawson wrote: > 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
