Hi Hiram, The /gbdb was last rsync on Aug 08 and we are referring to hg18 assembly. Our queries is that if we use the exact word 'uc001acj.1' in the position search in the Browser, we got an error mentioned by Wuqi but we are able to find the 'uc001acj.1' in the knownGene table in Hg18 database. Also if we go to the browser and search "chr1:938,741-939,777", we do see the ' uc001acj.1' in the link and description when clicking on it. Pls see attached for the print screen of it.
Pls advise. Thanks & Regards, Jack Ow Database Analyst Scientific Computing Group -----Original Message----- From: WANG Wuqi Sent: Wednesday, April 08, 2009 5:58 PM To: 'Hiram Clawson' Cc: [email protected]; Atif SHAHAB; OW Jack Ling; LEE Seow Eng; WANG Wuqi Subject: RE: Search errors in GBrowser 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 >> >> >> >> >
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