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
