Hi Narmala, The command line version of liftOver does accept gtf format. You can download it for Mac or Linux here: http://hgdownload.cse.ucsc.edu/admin/exe/
Alternatively, you can upload your data as a custom track and use the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) to output it as bed. Just go the Table Browser and click the "add custom tracks" button, add the data as a custom track, and select output format: BED, and click get output. - Greg On 6/20/11 11:48 AM, Akula, Nirmala (NIH/NIMH) [C] wrote: > Hi Katrina, > > Thank you very much for your response. The liftOver tool takes only > bed format. I am looking for a GTF format of RNA genes on build hg19. Any > suggestions will be really appreciated. > > 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: Katrina Learned [mailto:[email protected]] > Sent: Friday, June 17, 2011 9:06 PM > To: Akula, Nirmala (NIH/NIMH) [C] > Cc: '[email protected]' > Subject: Re: [Genome] FW: hg19 - RNA genes > > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
