Glad you figured it out! -- Brooke Rhead UCSC Genome Bioinformatics Group
Nguyen, Anh-Dao (NIH/NHGRI) [C] wrote: > Thanks, it has been solved. > I forget to change db to hg18 database. > > Anh-Dao > > > > -----Original Message----- > From: Nguyen, Anh-Dao (NIH/NHGRI) [C] > Sent: Tue 10/28/2008 8:05 AM > To: Brooke Rhead > Cc: [email protected] > Subject: RE: [Genome] pslMap & genePredToPsl > > 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
