Hello, Alex. We have just released the sacCer3 to sacCer2 liftOver file. You can now use the browser to perform this liftOver and the file is also available for download at: http://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/liftOver/.
Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Alex Lancaster Sent: Tuesday, November 08, 2011 1:46 PM To: [email protected] Subject: [Genome] over.chain file for converting SacCer3 -> SacCer2 Hi there, I need to translate some GFF3 (and/or BED) files from the chromosome co-ordinates used in the current S. cerevisiae assembly (circa 2011) back into the co-ordinates for the SacCer2 assembly (June 2008). This is because all the rest of the data I'm analysing are aligned to the (older) SacCer2 assembly. The datasets are the ribosomal profiling data from Ingolia et al. (2009). The raw files are available via SGD in both GFF3 and BED format: http://downloads.yeastgenome.org/published_datasets/Ingolia_2009_PMID_192138 77/track_files/ I know I can use liftOver to convert co-ordinates in a GFF3/BED file using a chain file that maps the co-ordinates of one assembly to another. However I didn't find any such chain files here: http://hgdownload.cse.ucsc.edu/downloads.html#yeast In addition the online version: http://genome.ucsc.edu/cgi-bin/hgLiftOver appears to allow you to convert from old assemblies (e.g. SacCer2) to new assemblies (e.g. SacCer3), but not the other way around. I need to do this because the new Ingolia data is aligned (presumably) to the most recent assembly (see link above), but I need it in SacCer2 co-ords. As suggested on http://genome.ucsc.edu/FAQ/FAQdownloads.html I am e-mailing you to request a generation of such an over.chain file. Best regards, Alex -- Alex Lancaster, Ph.D. Whitehead Institute for Biomedical Research _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
