Hi Yongsheng, geneName is a Genbank table, so is associated with all GenBank tracks. Whenever gbCdnaInfo is the selected table (the "top" defined table), geneName will appear as a linked table below.
One way to find it is: mRna track -> describe table schema -> click on gbCdnaInfo in associated tables -> geneName will now appear in the list of linked tables Thanks! Jennifer On 5/11/10 12:26 PM, Yongsheng Bai wrote: > Under which group/track that table "geneName" is located? > > -----Original Message----- > From: Jennifer Jackson [mailto:[email protected]] > Sent: Tuesday, May 11, 2010 2:46 PM > To: [email protected] > Cc: 'Antonio Coelho'; [email protected] > Subject: Re: [Genome] download hg18 genomic sequences > > Hello Yongsheng, > > The table refGene has two fields: > name = Genbank accession (nuc) > name2 = gene name > > The table gbCdnaInfo has two fields: > acc = Genbank accession (nuc) > gi = Genbank identifier > > The table geneName has two fields: > id = linking number into gbCdnaInfo.geneName > name = gene name as listed in the Genbank data sheet (note: RefSeq > sequences will have this as well as many mRNA sequences. It just depends > on what the data submission included.) > > To link in more identifiers based on UCSC Genes, which includes RefSeq > as an input, use the table kgXref. Please note that any RefSeq sequences > that have been added since the last UCSC Gene track update (2009-10-08 > for hg19) will not be included in the UCSC Gene track's tables (includes > kgXref). You will not find mRna or other Genbank accessions in this > table, but you will find data from the other sources used to build the > UCSC Genes track. See the UCSC Genes track description for details about > sources/last update. > > To find/explore the schema yourself, open up the Table browser to the > target genome, select a track/table, then use the "describe table > schema" button. The table selected will be defined, followed by linked > tables (including what keys they are linked on to the selected table > above). Any of this can be clicked on to "promote" them to become the > select table. Fewer or less linked tables may come up. This is an > excellent way to navigate the schema and find out what data is available > in which tables. > > Hopefully this is helpful! > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 5/11/10 7:19 AM, Yongsheng Bai wrote: >> Hello, >> >> Thanks! What's UCSC table name for converting "GenBank ID" to "Entrez >> ID/Gene symbol"? >> >> Thanks, >> YB >> >> -----Original Message----- >> From: Antonio Coelho [mailto:[email protected]] >> Sent: Thursday, May 06, 2010 3:09 PM >> To: [email protected] >> Cc: [email protected] >> Subject: Re: [Genome] download hg18 genomic sequences >> >> Hello Yongsheng, >> There is no limit to the size of the files, but as you have noticed, >> larger files to tend to load very slowly. >> One alternative is to convert your files to the bigBed format. You can >> read about here: >> >> http://genome.ucsc.edu/FAQ/FAQformat.html#format1.5 >> http://genome.ucsc.edu/goldenPath/help/bigBed.html >> >> You could also try breaking up your file into a group of smaller bed > files. >> >> I hope this answers your question. Please feel welcome to contact us > again. >> >> Antonio Coelho >> UCSC Genome Bioinformatics Group >> >> Yongsheng Bai wrote: >>> Hi, >>> >>> Is there any file size limit for loading a bed file into UCSC's custom >>> track? I am loading a ~200MB file, it takes forever... >>> >>> Thanks. >>> YB >>> >>> -----Original Message----- >>> From: Jennifer Jackson [mailto:[email protected]] >>> Sent: Monday, May 03, 2010 2:17 PM >>> To: [email protected] >>> Subject: Re: [Genome] download hg18 genomic sequences >>> >>> Hello, >>> >>> The track GC Percent may be helpful. It is based on the >>> reference genome. >>> >>> quote from GC Percent track description page: Description >>> >>> The GC percent track shows the percentage of G (guanine) >>> and C (cytosine) bases in 5-base windows. High GC content >>> is typically associated with gene-rich areas. >>> >>> You could BLAT your sequence against the reference genome >>> and view the region or note the coordinates, then export >>> data from this track using the Table browser. >>> >>> Or for batch use, if you know the coordinates, upload them >>> into the region filter in the Table browser and export data >>> from the GC Percent track or use the file from downloads (below). >>> >>> To this in batch on the command line to generate GC content for your own >>> sequences, use the utility percentage from the kent source tree. It >>> would take input data that you format. Please ask if you need help to >>> convert your files to the required formats. >>> >>> Table browser help: >>> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html >>> >>> Link to description of utilities (scroll to hgGcPercent): >>> http://hgwdev.cse.ucsc.edu/~larrym/utilities.html >>> >>> Download source: >>> http://genome.ucsc.edu/FAQ/FAQdownloads.html#download27 >>> >>> File formats: >>> http://genome.ucsc.edu/FAQ/FAQformat.html >>> >>> Complete GC content file for latest human reference genome: >>> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/gc5Base/ >>> >>> Best wishes with your project, >>> Jennifer >>> >>> ps: It would be best if you would send new questions directly to the >>> mailing list at [email protected]. This helps us to get you the >>> quickest reply. >>> >>> --------------------------------- >>> Jennifer Jackson >>> UCSC Genome Informatics Group >>> http://genome.ucsc.edu/ >>> >>> On 5/3/10 10:30 AM, Yongsheng Bai wrote: >>> >>>> Hi Jennifer, >>>> >>>> Does the UCSC allow or have the functionality to view/calculate GC >>>> >>> contents >>> >>>> given an input sequence? >>>> >>>> Thanks, >>>> YB >>>> >>>> >>> >>> >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
