Hello, If the sequences are not in the RefSeq track, then the RefSeq track tables will return no data. It appears that your IDs are not RefSeqs.
Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/12/10 6:36 AM, Yongsheng Bai wrote: > Hello, > > I would not be able to get the Entrez ID from GenBanl ID, it does not matter > whichever table I tried to combine (mm9.kgXref.refseq (via gbCdnaInfo.acc); > mm9.refGene.name (via gbCdnaInfo.acc); mm9.refLink.mrnaAcc (via > gbCdnaInfo.acc)). The rest of columns are always "n/a". > > Do you know why? Thanks!! > > =============== > > #mm9.gbCdnaInfo.acc mm9.gbCdnaInfo.geneName mm9.geneName.id > mm9.geneName.name mm9.refLink.geneName mm9.refLink.locusLinkId > AB004856 1 1 thrB n/a n/a > AB005263 2 2 argA n/a n/a > AB011407 0 0 n/a n/a n/a > AB012144 3 3 sam-pr n/a n/a > AB012145 0 0 n/a n/a n/a > AB017109 5 5 hacA n/a n/a > AB019621 0 0 n/a n/a n/a > AB026157 0 0 n/a n/a n/a > AB027742 6 6 nifH n/a n/a > AB027743 6 6 nifH n/a n/a > AB027744 6 6 nifH n/a n/a > AB027745 6 6 nifH n/a n/a > AB027746 6 6 nifH n/a n/a > AB027747 6 6 nifH n/a n/a > AB027748 6 6 nifH n/a n/a > AB027749 6 6 nifH n/a n/a > AB027750 6 6 nifH n/a n/a > AB045977 0 0 n/a n/a n/a > AB062062 0 0 n/a n/a n/a > AB062753 0 0 n/a n/a n/a > AB071366 7 7 azr n/a n/a > AB071367 7 7 azr n/a n/a > AB071368 7 7 azr n/a n/a > AB088633 8 8 enolA n/a n/a > AB094433 9 9 LipL32 n/a n/a > AB094434 9 9 LipL32 n/a n/a > AB094435 9 9 LipL32 n/a n/a > AB094436 9 9 LipL32 n/a n/a > AB094437 9 9 LipL32 n/a n/a > AB099701 10 10 comS n/a n/a > AB109116 11 11 SsgB n/a n/a > AB166870 12 12 SshEstI n/a n/a > AB176840 14 14 gyrB n/a n/a > AB240674 19 19 lipL41 n/a n/a > AB240675 19 19 lipL41 n/a n/a > AB240676 19 19 lipL41 n/a n/a > AB240677 19 19 lipL41 n/a n/a > AB240678 19 19 lipL41 n/a n/a > AB240679 20 20 lipL45 n/a n/a > AB240680 20 20 lipL45 n/a n/a > AB240681 20 20 lipL45 n/a n/a > AB240682 20 20 lipL45 n/a n/a > AB240683 20 20 lipL45 n/a n/a > > > > -----Original Message----- > From: Jennifer Jackson [mailto:[email protected]] > Sent: Tuesday, May 11, 2010 4:32 PM > To: [email protected] > Cc: 'Antonio Coelho'; [email protected] > Subject: Re: [Genome] download hg18 genomic sequences > > Hello - > > Locus Link IDs have been retired at NCBI. They have been replaced with > Entrez Genes. We retain the older table names/labels as LocusLink in our > database for convenience reasons, but the content is Entrez. > > Thanks, > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 5/11/10 1:08 PM, Yongsheng Bai wrote: >> 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
