Is locusLinkId in refFlat table referred to Entrez ID? -----Original Message----- From: Jennifer Jackson [mailto:[email protected]] Sent: Tuesday, May 11, 2010 4:02 PM To: [email protected] Cc: 'Antonio Coelho'; [email protected] Subject: Re: [Genome] download hg18 genomic sequences
Hello - The Table browser can link files if you do not just wish to download and process them yourself. Start with a base track (like mRNA), use output = "selected fields from primary and related tables", name file, and click on "get output". The next form will allow you to then link in the other tables and select fields. A previous answer today has the path for a similar query that you can use as a template combined with the table information we have already discussed: https://lists.soe.ucsc.edu/pipermail/genome/2010-May/022216.html The Table browser user's guide has instructions for all functions: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#SelectedFields Best wishes with your project, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/11/10 12:51 PM, Yongsheng Bai wrote: > Hello Jennifer, > > What I really want is a joined table with Entrez ID, Gene symbol, GenBank > ID... > > Thanks, > YB > > -----Original Message----- > From: Jennifer Jackson [mailto:[email protected]] > Sent: Tuesday, May 11, 2010 3:35 PM > To: [email protected] > Cc: 'Antonio Coelho'; [email protected] > Subject: Re: [Genome] download hg18 genomic sequences > > 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
