Good evening Kyle: You do not need the genome browser site in operation to run automated alignments. All you need is the sequence .2bit file for the assembly you want to align to and the blat program. Align your SNP sequences with blat to the 2bit file and you have your alignments. Take a look at the blat help message when you run that program without arguments.
--Hiram ----- Original Message ----- From: "Kyle Tretina" <[email protected]> To: "UCSC" <[email protected]>, "Pattle Pun" <[email protected]> Sent: Tuesday, January 19, 2010 5:13:04 PM GMT -08:00 Tijuana / Baja California Subject: [Genome] Mirror Site Question To whom it may concern, I am an intern at Wheaton College trying to create a mirror site for the UCSC genome browser so that I can attempt the automation of the alignment of SNP sequences in hg19 on chr16 only. I have a list of rs numbers to accomplish this and would not like to have to do them all manually on your site. I have two questions concerning this: 1) In step 4, what is the minimal /gbdb file area needed if I am only interested in hg19, chr16? The whole gbdb file area seems to be terrabytes. 2) In step 5 I am supposed to create a gbdb data file area and a database table area. How do I determine what files are needed for the database table area? Kyle Tretina Wheaton College _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
