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
