Hello I was wondering if this feature has become available
Thanks Valeria Hi Valeria, We appreciate your suggestion and will pass this request on to our developers. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 11/16/10 1:10 PM, Vasta, Valeria wrote: > Hello > > I wonder if you could consider adding a coordinate to gene name > feature.This is highly desirable for instance in the context of exon > capture and sequencing where you may have to figure out what gene it is > a certain region with poor coverage without bioinfo support > > Thanks > > Valeria > > -----Original Message----- > From: Katrina Learned [mailto:[email protected]] > Sent: Friday, October 29, 2010 3:01 PM > To: Vasta, Valeria > Cc: [email protected] > Subject: Re: [Genome] POISTION TO GENE NAME > > Hi Valeria, > > Unfortunately, the table browser isn't able to display the gene regions > you defined in the "define regions" option in the output. However, as > you are selecting fields you want as part of your output, in addition to > > the kgXref fields that my colleague Vanessa suggested, also select the > position fields from the knownGene table such as chrom, txStart and > txEnd. This way, your table browser output will contain the gene > positions, and you can group the genes by region yourself. > > Please don't hesitate to contact the mail list again if you have any > further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > Vasta, Valeria wrote, On 10/28/10 17:31: > >> Thank you so much, something I has selected before prevented to see >> that output format >> >> If I can ask one more question: how can I see the gene region I >> > defined > >> in define regions next to the geneSymbol - I need to figure out >> specifically which gene is each of those regions >> >> >> Valeria >> -----Original Message----- >> From: Vanessa Kirkup Swing [mailto:[email protected]] >> Sent: Thursday, October 28, 2010 4:30 PM >> To: Vasta, Valeria >> Cc: [email protected]; Pauline Fujita >> Subject: Re: [Genome] POISTION TO GENE NAME >> >> Dear Valeria, >> >> I think you are missing a step. Let's go through this step by step. >> >> Set the following: >> >> group: Genes and Gene Prediction Tracks >> track: UCSC genes >> table: knownGene >> >> >> You can paste in regions by clicking on "define regions". >> >> Then select: >> >> output format: "selected fields from primary and related tables" >> >> Click on "get output" >> >> Select: kgXref >> >> Scroll down and click on "Allow Selection From Checked Tables" >> >> This will allow you to select from something similar to these options: >> >> kgID Known Gene ID >> mRNA mRNA ID >> spID SWISS-PROT protein Accession number >> spDisplayID SWISS-PROT display ID >> geneSymbol Gene Symbol >> refseq RefSeq ID >> protAcc NCBI protein Accession number >> description Description >> >> I'm guessing that you would like the geneSymbol? If so check the box >> > and > >> click on "get output". >> >> I hope that this helps clarify things. Please feel free to contact the >> mailing list if you have further questions. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> >> >> ----- Original Message ----- >> From: "Valeria Vasta"<[email protected]> >> To: "Pauline Fujita"<[email protected]> >> Cc: [email protected] >> Sent: Thursday, October 28, 2010 12:02:06 PM GMT -08:00 US/Canada >> Pacific >> Subject: Re: [Genome] POISTION TO GENE NAME >> >> Hello >> >> I need to obtain the gene name=official symbol for certain >> > coordinates, > >> with the instructions below I do not get the option of output format: >> "selected fields from primary and related tables" >> >> So if I chose UCSC genes in the bed file I get the name of the UCSC >> > gene > >> - if I chose RefSeq I get the NM # if I chose CCDS I get the CCDS #. >> None of them gives me back the Official gene name >> >> Can you kindly let me know if there's any option that I haven't foun? >> >> Thanks >> >> Valeria >> >> -----Original Message----- >> From: Pauline Fujita [mailto:[email protected]] >> Sent: Wednesday, October 27, 2010 12:57 PM >> To: Vasta, Valeria >> Cc: [email protected] >> Subject: Re: [Genome] POISTION TO GENE NAME >> >> Hello Valeria, >> >> To input a batch of regions and output a list of gene names go to the >> table browser and after selecting your assembly of interest select: >> >> group: Genes and Gene Prediction Tracks >> track: UCSC genes >> table: knownGene >> >> You can paste in regions by clicking on "define regions". >> >> Then select: >> >> output format: "selected fields from primary and related tables" >> >> Once you click on "get output" this will take you to a menu where you >> can specify which fields you want to retrieve from associated tables. >> Now in the "...kgXref fields" section you can select "geneSymbol" or >> other indentifiers of interest to be included in the output. Then >> > click > >> "get output". >> >> Hopefully this information was helpful and answers your question. If >> > you > >> have further questions or require clarification feel free to contact >> > the > >> mailing list at [email protected]. >> >> Regards, >> >> Pauline Fujita >> UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu >> >> >> >> On 10/27/10 10:54, Vasta, Valeria wrote: >> >> >>> Hello >>> >>> >>> I tried to get the name of the genes but did not succeed. I tried >>> >>> >> refseq >> >> >>> but I get the NM_... numbers or Geneid but none gives me back the >>> > Gene > >>> name >>> >>> Valeria >>> >>> -----Original Message----- >>> From: Katrina Learned [mailto:[email protected]] >>> Sent: Monday, October 18, 2010 8:38 AM >>> To: Vasta, Valeria >>> Cc: [email protected] >>> Subject: Re: [Genome] POISTION TO GENE NAME >>> >>> Hi Valeria, >>> >>> To search the Genome Browser using a list of chromosome regions, >>> first create a custom track of the regions. You will then be able to >>> intersect your custom track with the gene track of interest using the >>> Table Browser. Help on creating a custom track is located here: >>> >>> http://genome.ucsc.edu/goldenPath/help/customTrack.html >>> >>> For a simple list of chromosome positions, use BED format, described >>> here: >>> >>> http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED >>> >>> Once the custom track has been created, go the the Table Browser and >>> select the gene track from which you wish to the retrieve gene names. >>> Hit the "intersection: create" button and select your new custom >>> >>> >> track. >> >> >>> Choose one of the intersection options listed under "These >>> combinations will maintain the gene/alignment structure (if any) of >>> >>> >> [the >> >> >>> gene track]". Hit "submit", then choose "output format: BED" and get >>> the output. You should get all records from the gene table you >>> >>> >> selected >> >> >>> (including their positions) that intersect with your custom track. >>> >>> I hope this is helpful. >>> >>> Katrina Learned >>> UCSC Genome Bioinformatics Group >>> >>> >>> Vasta, Valeria wrote, On 10/15/2010 10:04 AM: >>> >>> >>>> Hello >>>> >>>> >>>> >>>> Is it possible to batch search with positions to get gene names? >>>> >>>> thanks >>>> >>>> >>>> >>>> Valeria Vasta >>>> >>>> Assay Development Scientist | Biochemical and Molecular Genetics R&D >>>> >>>> Seattle Children's Research Institute >>>> >>>> 206-884-7674 OFFICE >>>> >>>> 206-987-7660 FAX >>>> >>>> [email protected] >>>> >>>> OFFICE 1900 9th Ave, Seattle, WA 98101 >>>> >>>> MAIL C9S-9 >>>> >>>> WWW seattlechildrens.org<http://seattlechildrens.org/> >>>> >>>> >>>> >>>> >>>> >>>> CONFIDENTIALITY NOTICE: This e-mail message, including any >>>> >>>> >>> attachments, is for the sole use of the intended recipient(s) and may >>> contain confidential and privileged information protected by law. >>> > Any > >>> unauthorized review, use, disclosure or distribution is prohibited. >>> >>> >> If >> >> >>> you are not the intended recipient, please contact the sender by >>> > reply > >>> e-mail and destroy all copies of the original message. >>> >>> >>>> _______________________________________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>> >>>> >>>> >>> CONFIDENTIALITY NOTICE: This e-mail message, including any >>> >>> >> attachments, is for the sole use of the intended recipient(s) and may >> contain confidential and privileged information protected by law. Any >> unauthorized review, use, disclosure or distribution is prohibited. >> > If > >> you are not the intended recipient, please contact the sender by reply >> e-mail and destroy all copies of the original message. >> >> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >>> >> >> >> CONFIDENTIALITY NOTICE: This e-mail message, including any >> > attachments, > >> is for the sole use of the intended recipient(s) and may contain >> confidential and privileged information protected by law. Any >> unauthorized review, use, disclosure or distribution is prohibited. >> > If > >> you are not the intended recipient, please contact the sender by reply >> e-mail and destroy all copies of the original message. >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> CONFIDENTIALITY NOTICE: This e-mail message, including any >> > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information protected by law. Any > unauthorized review, use, disclosure or distribution is prohibited. If > you are not the intended recipient, please contact the sender by reply > e-mail and destroy all copies of the original message. > >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > > CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
