Thanks Deanna, This is good information to share. We will be pulling the updated cow genome from UCSC and including in the full genome name the exact source/release notation, along with the short label that UCSC assigns. This information is already in the Galaxy builds list for the cow genomes - including those without data yet incorporated (the builds list is a pull-down menu on the 'Edit attributes' form, reached by clicking on the pencil icon, or by assigning a database when uploading a file). Enter "bos" into the search box for a list. For individual tools, we tend to just use the short label to keep the tool forms less cluttered. The short labels we use are the most common identifier for genomes (when available) and are unique. When we create them, we tend to use a 'Genus_species_build-identifier' type of nomenclature. For the full credits/details about how any UCSC genome was put together (and by whom), the "Credits" page at the UCSC Browser should be referenced, along with the README files on their Downloads server. For non-UCSC Genomes, the full genome name includes enough details about the specific release to locate the source and find similar information. We don't do any chromosome renaming, so there is very little to nothing specific to declare in terms of processing credits on the Galaxy side, we basically just obtain the genome and integrate it as-is using the same methods as declared in the local NGS setup wiki. Great to clarify this information! Jen Galaxy team On 3/27/12 11:58 AM, Church, Deanna (NIH/NLM/NCBI) [E] wrote:

Note: People should be aware that the cow reference has changed. The old cow reference was based on Btau_4.1 (from Baylor) and the new one is based on UMD 3.1 (from UMD) so there are likely to be lots of changes. There is an updated cow assembly from Baylor (Btau_4.6) that includes the Y chromosome.

UMD 3.1: http://www.ncbi.nlm.nih.gov/genome/assembly/313678/ Btau_4.6.1: http://www.ncbi.nlm.nih.gov/genome/assembly/313728/

Deanna

On 3/27/12 2:22 PM, "Jennifer Jackson"<jen@bx.psu.edu> wrote:

...

Hi Elihu,

The latest cow genome (along with a few others) are on our active to do list and are planned to be on the public Galaxy server near term.

Meanwhile, you can obtain the genome from UCSC and use it as custom genome with TopHat. Instructions are in this wiki: http://wiki.g2.bx.psu.edu/Learn/CustomGenomes

We plan to announce the addition of new genomes via Twitter. If you don't follow Twitter, the Galaxy Update and Twitter wiki pages will also note these additions as they are included: http://wiki.g2.bx.psu.edu/GalaxyUpdates http://wiki.g2.bx.psu.edu/Galaxy%20on%20Twitter

Best,

Jen Galaxy team

On 3/27/12 3:56 AM, Aranday-Cortes, Elihu wrote:

...

Hi Galaxy Team,

I'd like to use Tophat but the last version of the cow genome is not listed (BotsTau7). Tha last version is listed is BosTau4 . any chance for an update?

Thanks

Elihu

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The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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