Question: Using the S. cerevisiae (sacCer3) reference genome with snpEff
0
gravatar for rcocklin
3.2 years ago by
rcocklin0
United States
rcocklin0 wrote:

Hello-

I'm trying to using snpEff to analyze the effects of SNPs and Indels on yeast protein coding genes.  After reading many posts here, I now understand there are very limited options for using snpEff on Galaxy Main.  So, I set up a Cloud Instance of Galaxy and loaded the latest version of snpEff (4.0) from the tool shed.  Unfortunately, the most recent version of the Saccharomyces cerevisiae reference genome (sacCer3) is not available.  In fact, I don't think any S. cerevisiae genome is available.  The available genomes can be downloaded using the tool snpEff Download (version 4.0).  This tool indicates available genomes can be found at https://snpeff-data.galaxyproject.org/databases/v4_0/.  Is it possible to include the sacCer3 reference genome here so that snpEff Download can use it?

Thank you,

Ross

snpeff • 1.2k views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by rcocklin0

I need this as well. thanks

ADD REPLYlink written 22 months ago by jnpitt10

Hello, Galaxy Main (http://usegalaxy.org) is now unlikely to be updated to include this build. However, installing the prior tool version on a local or cloud Galaxy and configuring for this genome is still an option.

Thanks, Jen, Galaxy team

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

S. cerevisie is available for an earlier version of snpEff here:
https://snpeff-data.galaxyproject.org/databases/v3_6/

A Trello ticket has been created to review adding the genome for the latest builds. Please follow the same for updates. https://trello.com/c/uE4ByUg2

Best, Jen, Galaxy team 

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k
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