Great, I forgot about those...however, it still doesn't tell me what was actually downloaded from SGD...
On Wed, Sep 9, 2009 at 6:14 PM, Jennifer Jackson <[email protected]> wrote: > Hello, > > The details of the assembly are at the bottom of the Yeast sacCer2 gateway > page. Click through the "Sequences" link to see the actual list of data. > > The data for download using ftp is here: > http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/bigZips/ > > For the multiz7way, click on the track's name from within the sacCer2 > assembly browser for details about the processing, including methods, > inputs, and references. > > We hope this helps, > > Jennifer > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "kenny daily" <[email protected]> wrote: > > > From: "kenny daily" <[email protected]> > > To: [email protected] > > Cc: "Suzanne Sandmeyer" <[email protected]> > > Sent: Wednesday, September 9, 2009 2:13:03 PM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] Details about sacCer2 and multiz7way > > > > Can someone provide more details about the sacCer2 genome and > > multiple > > alignment multiz7way? How does it match up with the data that is in > > SGD, > > displayed in their genome browser, etc.? The info site says: > > > > "The June 2008 (*Saccharomyces cerevisiae*) genome assembly is based > > on > > sequence dated June 2008 in the Saccharomyces Genome > > Database<http://www.yeastgenome.org/>(SGD)." > > > > Interestingly, nothing in any of the given download directories are > > dated > > June 2008 - where did this date come from? > > > > If one looks at SGD's download site ( > > > http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/ > ) > > there are some chromosomes listed at June 2008. However, not all the > > chromosomes in the download directory are dated June 2008 - some are > > earlier, and some even later. For example: > > > > chr10.fsa< > http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/chr10.fsa > >18-Feb-2009 > > 15:38 740K > > > > What is the exact list of chromosome files used to build the sacCer2 > > sequence and multiz7way alignment? > > > > For the other genomes in the multiz7way its easier, as there is a > > single, > > tar gzipped file for the genome. Is there a way that this type of > > download > > can be provided for the sacCer2 data? > > > > Not having exact, replicable instructions for generating and > > disseminating > > data makes publication and building other tools very difficult. It > > would > > benefit the community as a whole for some more cooperation between SGD > > (or > > WormBase, etc.) and the UCSC site, at least so that a user can tell > > WHAT > > data is being used WHERE and WHEN, three keywords for > > reproducibility. > > > > Thank you very much for any information and assistance. > > > > -- > > Kenny Daily > > [email protected] > > http://www.kennydaily.net/ > > > > --- Prediction is very difficult, especially about the future. (Niels > > Bohr) > > --- > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > -- Kenny Daily [email protected] http://www.kennydaily.net/ --- Prediction is very difficult, especially about the future. (Niels Bohr) --- _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
