Hi Nirmala, To get the Human RNA genes track on hg19, you could do a liftOver from hg18 to hg19. Please see this information about liftOver (you'll want to follow the second part about downloading/using the command line version of the liftOver tool): http://genome.ucsc.edu/FAQ/FAQdownloads.html#download28
If you are open to using another track, the Gencode Genes has many non-coding RNAs, and you can filter that track to only show certain transcript types: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencode Another track that might be of interest to you is the sno/miRNA track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgRna Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Akula, Nirmala (NIH/NIMH) [C] wrote, On 6/17/2011 9:59 AM: > Dear Pauline, > > Below is the response I received from Dr. Eddy. Could you please > suggest any alternatives to get RNA genes track for hg19? > > Thank you very much. > > Best Regards, > Nirmala > > ------------------------------------------------------------------------------------ > Nirmala Akula, MS, PhD > Contractor, > Human Genetics Branch > NIMH/NIH > Blg 35, Rm 1A/205 > Bethesda, MD - 20892 > Phone# 301-451-4258 > > -----Original Message----- > From: Eddy, Sean [mailto:[email protected]] > Sent: Friday, June 17, 2011 12:56 PM > To: Akula, Nirmala (NIH/NIMH) [C] > Subject: Re: [Genome] hg19 - RNA genes > > I'm sorry, UCSC is mistaken. We did not produce annotation for hg19. Our > annotation of hg16, the last assembly we annotated (Mar 2004), is here: > ftp://selab.janelia.org/pub/annotation/human-hg16 > > Sean > > ----- > Sean Eddy | HHMI Janelia Farm Research Campus | http://selab.janelia.org/ > > > > > On Jun 17, 2011, at 12:35 PM, Akula, Nirmala (NIH/NIMH) [C] wrote: > >> Dear Dr. Eddy, >> >> I wanted to download RNA genes (hg19) data from UCSC genome browser, >> but it was unavailable. I e-mailed UCSC bioinformatics team and they asked >> me to contact you. Could you please let me know when RNA genes track will be >> available for hg19 build? >> Thank you very much. >> >> Best Regards, >> Nirmala >> >> ------------------------------------------------------------------------------------ >> Nirmala Akula, MS, PhD >> Contractor, >> Human Genetics Branch >> NIMH/NIH >> Blg 35, Rm 1A/205 >> Bethesda, MD - 20892 >> Phone# 301-451-4258 >> >> -----Original Message----- >> From: Pauline Fujita [mailto:[email protected]] >> Sent: Thursday, June 16, 2011 3:29 PM >> To: Akula, Nirmala (NIH/NIMH) [C] >> Cc: '[email protected]' >> Subject: Re: [Genome] hg19 - RNA genes >> >> Hello Nirmala, >> >> If you are interested in seeing a version of this track for hg19 you >> should contact Sean Eddy at Washington University, the original source >> for the data behind this track. >> >> You can read more about this track on its associated description page: >> >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&c=chrX&g=rnaGene >> >> Best regards, >> >> Pauline Fujita >> UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu >> >> >> On 06/15/11 14:14, Akula, Nirmala (NIH/NIMH) [C] wrote: >>> Hi, >>> >>> I would like to download Human RNA genes in hg19 assembly. >>> Could you please let me know when track is going to be available? >>> >>> Thank you very much. >>> >>> Best Regards, >>> Nirmala >>> >>> ------------------------------------------------------------------------------------ >>> Nirmala Akula, MS, PhD >>> Contractor, >>> Human Genetics Branch >>> NIMH/NIH >>> Blg 35, Rm 1A/205 >>> Bethesda, MD - 20892 >>> Phone# 301-451-4258 >>> >>> _______________________________________________ >>> 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
