Hello Broke, Thanks for your reply.
I was able to connect to the UCSC's public database using mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A However, when I ran the genePredToPsl program as you suggested: genePredToPsl -bedFormat db toNISC_allPhase2_all_liftover fileOut.psl and created a .hg.conf file containing db.host=genome-mysql.cse.ucsc.edu db.user=genomep db.password=password I got the following error message: Loading gene predictions. Doing conversion. Couldn't connect to database db on genome-mysql.cse.ucsc.edu as genomep. Access denied for user 'genomep'@'%' to database 'db' I did change the .hg.conf file permission to 600. Thanks for your help. Anh-Dao -----Original Message----- From: Brooke Rhead [mailto:[EMAIL PROTECTED] Sent: Fri 10/24/2008 4:23 PM To: Nguyen, Anh-Dao (NIH/NHGRI) [C] Cc: [email protected] Subject: Re: [Genome] pslMap & genePredToPsl Hello Anh-Dao, Thank you for searching the mailing list archives before asking your question. The genePredToPsl command needs a MySQL database to function: usage: genePredToPsl db file.gp fileOut.psl Using your same filenames, this would be: genePredToPsl -bedFormat db bedformatfile pslformatoutputfile Where "db" is the database name, such as hg18. Many tools in the Genome Browser source tree need access to a database. You could either set up your own database and put the appropriate tables in it (in this case the 'chromInfo' table is needed), or you can use the public MySQL server: http://genome.ucsc.edu/FAQ/FAQdownloads#download29 As described in the link above, you will need to put a file called .hg.conf in your home directory that contains these lines: db.host=genome-mysql.cse.ucsc.edu db.user=genomep db.password=password I hope this answers your question. If you have further questions, please feel free to email us again at [EMAIL PROTECTED] -- Brooke Rhead UCSC Genome Bioinformatics Group Nguyen, Anh-Dao (NIH/NHGRI) [C] wrote: > Hello, > > I would like to use the pslMap program. > After reading the threads below, firstly, I need to convert my human's SNPs > from BED format to PSL format using the genePredToPsl program > > http://www.soe.ucsc.edu/pipermail/genome/2006-May/010816.html > http://www.soe.ucsc.edu/pipermail/genome/2007-November/015074.html > > genePredToPsl -bedFormat bedformatfile pslformatoutputfile > > e.g. bedformatfile has the following entries: > chr6 32470491 32470780 BTNL2_NM_019602_exon_1 0 + > chr6 32471793 32472141 BTNL2_NM_019602_exon_2 0 + > > I am not sure how to use the command line above correctly. > > > Thanks for your help. > Anh-Dao > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
