Hi YB, Are you looking for the reference genome sequence, or for annotations on the reference genome? GTF is a format for annotations: http://genome.ucsc.edu/FAQ/FAQformat.html#format4
If you are looking for the chicken reference genome sequence, you can find it here: http://hgdownload.cse.ucsc.edu/goldenPath/galGal3/bigZips/ If you are looking for gene annotations in GTF format, you can get them from the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), but be aware of this problem with GTF-formatted Table Browser output: https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026236.html If you want to use Ensembl's gene annotations for chicken that are already in GTF format, you can get them directly from Ensembl: ftp://ftp.ensembl.org/pub/release-65/gtf/gallus_gallus/ Alternatively, you could use genePredToGtf to convert gene annotations from the Table Browser that you retrieve in genePred format (use "output format: all fields from selected table" to get most of the gene annotations in genePred format): https://lists.soe.ucsc.edu/pipermail/genome/2011-July/026507.html I hope this information is helpful. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 1/27/12 7:17 AM, Yongsheng Bai wrote: > Hello, > > Where and how can I locate/download chicken reference genome in GTF format > for cufflinks to read? > > Thanks, > YB > > -----Original Message----- > From: Kayla Smith [mailto:[email protected]] > Sent: Monday, July 06, 2009 5:42 PM > To: [email protected] > Subject: Re: [Genome] question > > > Hello YB, > > Try the table hg18.kgXref > > It is found here: > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ > > This page sometimes takes a while to load. > > Please let us know if you have any further questions. > > Kayla Smith > UCSC Genome Bioinformatics Group > > ----- "Yongsheng Bai"<[email protected]> wrote: > >> HI Kayla, >> >> Where can I download/find the correspondent table between HUGO gene >> symbol >> (i.e. TCF7L2) and the name (i.e. uc001aaa.2) for "knownGene" of UCSC >> Genes >> track? >> >> Thanks, >> YB >> >> -----Original Message----- >> From: Kayla Smith [mailto:[email protected]] >> Sent: Wednesday, July 01, 2009 7:38 PM >> To: [email protected] >> Cc: [email protected]; Jennifer Jackson >> Subject: Re: [Genome] question >> >> >> YB, >> >> You're very close to getting the answer. The missing step is to >> toggle the >> "output format" pulldown to "sequence". >> >> >> I hope this helps, >> >> Kayla Smith >> UCSC Genome Bioinformatics Group >> >> >> ----- "Yongsheng Bai"<[email protected]> wrote: >> >>> Hi Jennifer, >>> >>> Thanks for the response. But I didn't see any of tables under "Gene >>> and Gene >>> Prediction" track has the field for nucleotide sequence which codes >>> the >>> protein. Which table should I join with "KnownGene" or link to? >>> >>> Thanks, >>> YB >>> >>> -----Original Message----- >>> From: Jennifer Jackson [mailto:[email protected]] >>> Sent: Tuesday, June 30, 2009 5:01 PM >>> To: [email protected] >>> Cc: [email protected] >>> Subject: Re: [Genome] question >>> >>> Hello, >>> >>> The data would be contained in a "Gene and Gene Prediction" track. >>> Check >>> out the group's track contents using the Assembly browser (click on >> >>> track name for details (source/methods). UCSC Genes would be the >>> primary >>> recommended track). >>> >>> Once a target track is selected, follow the instructions here to >>> obtain >>> the data. Files in Downloads are named the same as in the Table >>> browser >>> - just add a .txt.gz for the data files and a .sql for the schema >>> files. >>> http://genome.ucsc.edu/FAQ/FAQdownloads#download1 >>> http://genome.ucsc.edu/FAQ/FAQdownloads#download31 >>> >>> Also, some details about using the Table browser and the data >> contents >>> >>> in the UCSC Gene's associated tables is contained in this earlier >>> mailing list response: >>> https://lists.soe.ucsc.edu/pipermail/genome/2009-June/019349.html >>> >>> Thank you, >>> Jennifer Jackson >>> UCSC Genome Bioinformatics Group >>> >>> Yongsheng Bai wrote: >>>> Dear Sir or Madam, >>>> >>>> >>>> >>>> How to download all human protein-coding genes' full coding region >> >>>> >>>> sequences (CDS) with the genomic coordinates for the beginning >> and >>> end of >>>> this CDS from the UCSC site? >>>> >>>> >>>> >>>> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
