Hello Mali, I see what you are talking about now. Thank you for clarifying.
I confirmed with our engineers that the "(lifted to sacCer2 from Ensembl version EF 2)" comment was only applicable to version 59 of Ensembl Genes on sacCer2. Versions 60, 61, and 62 are identical to Ensembl. The comment was incorrect and has been removed. Thank you for alerting us to this error, and sorry for the confusion! -- Brooke Rhead UCSC Genome Bioinformatics Group On 06/29/11 22:01, mali salmon wrote: > Dear Brooke > Thanks for your reply. I'm not on a mirror site, but using the main UCSC > site. > In order to download the gtf file I went to the table browser, and chose the > following: > genome: S.cerevisiae > assembly: June 2008, SGD/sacCer2 > group: Ensembl genes > track: ensGene > output format: GTF > When I click on the "Describe table schema" link I see: > "Schema for Ensembl Genes - Ensembl Genes *(lifted to sacCer2 from Ensembl > version EF 2*)" > Mali > > > On Wed, Jun 29, 2011 at 11:00 PM, Brooke Rhead <[email protected]> wrote: > >> Hi Mali, >> >> Can you be more specific about how you downloaded the file from the Table >> Browser? I only see regular (not lifed) version 62 Ensembl genes on the >> UCSC sacCer2 browser. >> >> Were you by any chance on a mirror site, and not on >> http://genome.ucsc.edu/? >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 06/29/11 03:15, mali salmon wrote: >> >>> Dear Sir/Madam >>> I have downloaded a gtf file for yeast ensembl genes from the ucsc table >>> browser. >>> According to the description of the table, the locations were "lifted to >>> sacCer2 from Ensembl version EF 2." >>> However, when I compare the locations I get to those from ensembl gtf file >>> I >>> downloaded from ensembl ("Saccharomyces_cerevisiae.**EF2. >>> 62.gtf), I see that there is no difference. >>> How this could be? I suppose there are some changes between the two builds >>> Looking forward to your reply >>> Thanks >>> Mali >>> ______________________________**_________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
