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Question: Upload Of Zea Mays Genome To Galaxy?
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gravatar for karlerhard@berkeley.edu
7.7 years ago by
karlerhard@berkeley.edu • 90
karlerhard@berkeley.edu • 90 wrote:
Hello, I'm interested in using the galaxy tools to analyze some transcriptome libraries I made of maize seedlings. Would it be possible to upload the maize reference genome to the galaxy browser? It's available at the following website: http://ftp.maizesequence.org/current/ Hope this can be done, would be really exciting! Thanks, Karl
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modified 7.7 years ago by Kelly Vincent • 340 • written 7.7 years ago by karlerhard@berkeley.edu • 90
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gravatar for Felix Hammer
7.7 years ago by
Felix Hammer • 200
Felix Hammer • 200 wrote:
Last time I checked there was an up to date zea mays genome already available in galaxy. Am 05.03.2011 21:49, schrieb karlerhard@berkeley.edu:
ADD COMMENT • link written 7.7 years ago by Felix Hammer • 200
Oh, I was a bit hasty I see... However, whereas I can see the maize reference genome in the pull down list if I try to use an actual tool with an uploaded file (eg. map with Bowtie), the maize genome option does not come up in the list for 'Database/Build' under the 'Edit Attributes' section for an uploaded file. thanks for help, karl
ADD REPLY • link written 7.7 years ago by karlerhard@berkeley.edu • 90
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gravatar for Kelly Vincent
7.7 years ago by
Kelly Vincent • 340
Kelly Vincent • 340 wrote:
Karl, Zea mays is available for use under the NGS tools. I did notice that it is not available as one of Galaxy's genome/database labels (such as on upload), but this is an oversight that will be corrected ASAP. You can still use the mapping tools in the meantime. Regards, Kelly
ADD COMMENT • link written 7.7 years ago by Kelly Vincent • 340
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gravatar for Kelly Vincent
7.7 years ago by
Kelly Vincent • 340
Kelly Vincent • 340 wrote:
Karl, Zea mays is now available as a general database/build label. The full value is "Zea_mays_B73_RefGen_v2", but searching for any part of that or "maize" will bring it up. Thanks for using Galaxy. Regards, Kelly
ADD COMMENT • link written 7.7 years ago by Kelly Vincent • 340
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