Whoops, never mind. I just figured it was reverse strand. Thank you! Woody
2010/11/17 Woody Lin <[email protected]> > Hi Hiram, > > Sorry to get back to you so late. Haven't had time to test if it is trackDb > table problem. Now, I have another question about the genomic position on > the genome browser. > > I spot that some of the codons are not consistent with the DNA sequence. > > For example, at chr10:91,404,661-91,404,663, the DNA sequence shows CGG and > should be "R", but the codons on both UCSC and RefSeq are "P". > > Could help me with the problem first? > > Thank you very much! > > > Sincerely, > Woody > > 2010/11/2 Hiram Clawson <[email protected]> > >> Good Morning Woody: >> >> Do you know where you got the trackDb table that only has 134 rows in it ? >> How do you create the trackDb table ? If you fetch our hg19 trackDb >> table, >> you should have at least 300 rows. >> >> We have a lot of mysteries here and I am thoroughly puzzled. We are going >> to need to get some of the kent source tree command built. Is your build >> functioning in your source tree ? Can you go to the directory >> src/hg/hgsql and build the hgsql command. Set up your $HOME/.hg.conf >> file with the instructions from src/product/README.mysql.setup >> and get the hgsql command functioning so you don't need to type >> user names and passwords with your mysql command. We also need >> $HOME/.hg.conf >> functioning so we can use other kent commands. Get the command hgTrackDb >> built in the directory src/hg/makeDb/hgTrackDb/ and hgFindSpec >> in src/hg/makeDb/hgFindSpec >> There may be other commands we need but this is a good start. >> >> Following the instructions in src/product/README.building.source >> to get the source tree built. >> >> I had assumed you have been using the source tree all along. Do you >> build the CGI binaries or copy ours ? >> >> --Hiram >> >> ----- Original Message ----- >> From: "Woody Lin" <[email protected]> >> To: "Hiram Clawson" <[email protected]> >> Cc: [email protected] >> Sent: Monday, November 1, 2010 10:51:31 PM GMT -08:00 US/Canada Pacific >> Subject: Re: [Genome] Question about installing genome browser (error: >> wgEncodeGisDnaPet) >> >> Dear Hiram, >> >> >> It looks like you are using hgsql instead of mysql, so I changed hgsql to >> mysql and got the following messages: >> >> >> >> My-Server: trackDb admin$ mysql -u root -p -e "select count(*) from >> trackDb;" hg19 >> Enter password: >> +----------+ >> | count(*) | >> +----------+ >> | 134 | >> +----------+ >> My-Server: trackDb admin$ make GIT=echo EXTRA=-strict DBS=hg19 alpha >> find . -type l -exec rm {} \; >> echo pull >> pull >> ./loadTracks -release=alpha trackDb hgFindSpec hg19 >> ./loadTracks: line 58: hgsql: command not found >> Note: database hg19 does not exist, skipping >> ./checkMetaDb alpha metaDb hg19 >> ./checkMetaDb: line 22: hgsql: command not found >> Note: database hg19 does not exist, skipping >> >> >> Woody >> >> 2010/11/2 Hiram Clawson < [email protected] > >> >> >> Good Morning Woody: >> >> Please try this command in your source tree directory >> src/hg/makeDb/trackDb/ >> >> $ hgsql -e "select count(*) from trackDb;" hg19 >> $ make GIT=echo EXTRA=-strict DBS=hg19 alpha >> $ hgsql -e "select count(*) from trackDb;" hg19 >> >> This load of the trackDb table with the -strict argument >> will load only tracks that actually have tables in your hg19 database. >> You should note the count of entries in the trackDb table will be >> lower after the 'make' command. >> >> --Hiram >> >> >> >> >> Woody Lin wrote: >> >> >> By the way, currently, I have only imported two databases "hg19" and >> "hgFixed". (all tables are imported) >> Do I need extra databases? >> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
