Cow Genome Update In Tophat

6.7 years ago by

United States

Jennifer Hillman Jackson ♦ 25k 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

ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 6.7 years ago by Church, Deanna (NIH/NLM/NCBI) [E] • 30

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

ADD REPLY • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k

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