Hi Hiram, Thanks a lot.
Is it from rsync://hgdownload.cse.ucsc.edu/mysql/hg18/ for tables updating? this means overwrite our all current mysql tables. Best & Regards Wuqi -----Original Message----- From: Hiram Clawson [mailto:[email protected]] Sent: Wednesday, April 08, 2009 2:16 PM To: WANG Wuqi Cc: [email protected] Subject: Re: Search errors in GBrowser You use the rsync command to fetch new data to update your gbdb and mysql tables. For example # cd /gbdb/hg18 # rsync -azP --stats rsync://hgdownload.cse.ucsc.edu/gbdb/hg18/ ./ Same idea for your mysql tables. Beware if you use the --delete option in case you have local data in your system. That would delete your local data. --Hiram WANG Wuqi wrote: > Hi Hiram, > > What organism genome assembly are you using ? > -- Human, mouse, zebrafish and medaka. > > The item 'uc001acj.1' can be searched in http://genome.ucsc.edu/. > > We use a private genome browser, how to update our tables and /gbdb/ ? > > > Thanks & Regards > > Wuqi > > > > -----Original Message----- > From: Hiram Clawson [mailto:[email protected]] > Sent: Tuesday, April 07, 2009 9:44 PM > To: WANG Wuqi > Cc: [email protected] > Subject: Re: Search errors in GBrowser > > What genome browser WEB site are you using ? > > What organism genome assembly are you using ? > > Both of your example searches appear to work just > fine at http://genome.ucsc.edu/ > > If this is your private genome browser, perhaps > your tables and /gbdb/ files need an update ? > > --Hiram > > WANG Wuqi wrote: >> >> >> Hi Hiram, >> >> >> >> In Gbrowser, to encounter below errors when search 'uc001acj.1': >> >> >> >> Sorry, couldn't locate uc001acj.1 in genome database >> >> >> >> But when try to search 'uc001aab.1', it is ok. >> >> >> >> i.e. some search can be done, some can not. >> >> >> >> >> >> And, when I search 'uc001acj.1', in MYSQL trace log file to find > below >> Mysql statements: >> >> ----------------------. >> >> 14553 Connect reado...@localhost on hg18 >> >> 14553 Quit >> >> 14552 Query select chrom,chromStart,chromEnd,name >> >> from DHP001fr_hg18_07032008_A_v1 where name like >> '%uc001acj.1%' >> >> 14554 Connect reado...@localhost on hg18 >> >> 14554 Quit >> >> 14552 Query select name,chrom,txStart,txEnd from knownGene >> >> where name in ("uc001acj.2") >> >> 14552 Query select kgID,geneSymbol,description >> >> from kgXref where kgID in ("uc001acj.2") >> >> 14555 Connect reado...@localhost on hg18 >> >> 14555 Quit >> >> 14552 Query select chrom,chromStart,chromEnd,name from > switchDbTss >> >> where name like 'uc001acj.1%' >> >> ----------------------. >> >> >> >> It is strange, I search "uc001acj.1", but see "uc001acj.2" in sql. >> >> >> >> >> >> Please help >> >> >> >> >> >> Thanks & Regards >> >> >> >> Wuqi >> >> >> >> > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
