upload of Zea mays genome to galaxy?
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
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:
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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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
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:
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
___________________________________________________________ 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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ 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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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 On Mar 5, 2011, at 3:49 PM, karlerhard@berkeley.edu 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
___________________________________________________________ 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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Felix Hammer -
karlerhard＠berkeley.edu -
Kelly Vincent