suggestions for de novo assembly plant transcriptome without reference
Dear Galaxy Expert, I would like to use Galaxy to de-novo assembly single-end read illumina data (140bp) for plant transcriptomes (without reference). I remember early emails mention trinity in Galaxy. But I could not see at Galaxy web http://main.g2.bx.psu.edu/root . Maybe it is installed in Amarzon EC2? Other suggestions in de-novo assembly plant transcriptomes without reference. Many thanks and look forward to hearing back from you, Jane <galaxy-user@bx.psu.edu>
Hi Jane, I have used Trinity on a local installation here at Bristol University. The main reason its not on Galaxy main is because its very very memory intensive (we run it on nodes with 256GB RAM). So you really need access to a big machine to run it. Having said all that the output is astoundingly good so it's worth the time and effort to get a run going if you can. Cheers David On 21 Dec 2011, at 13:36, Jane Song wrote:
Dear Galaxy Expert,
I would like to use Galaxy to de-novo assembly single-end read illumina data (140bp) for plant transcriptomes (without reference). I remember early emails mention trinity in Galaxy. But I could not see at Galaxy web http://main.g2.bx.psu.edu/root . Maybe it is installed in Amarzon EC2? Other suggestions in de-novo assembly plant transcriptomes without reference.
Many thanks and look forward to hearing back from you, Jane
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Baohua and Jane, As David noted, there is a Trinity wrapper for Galaxy, it works, and Trinity is great. However, Trinity is not enabled/installed on our public server (main.g2) or on Galaxy cloud instances (Amazon) right now. You'll need a little programming expertise to set up Trinity locally or on the cloud. Also, the Galaxy's team support for Trinity is very minimal right now as we haven't done much testing with it yet. Good luck, J. On Dec 21, 2011, at 4:01 PM, David Matthews wrote:
Hi Jane,
I have used Trinity on a local installation here at Bristol University. The main reason its not on Galaxy main is because its very very memory intensive (we run it on nodes with 256GB RAM). So you really need access to a big machine to run it. Having said all that the output is astoundingly good so it's worth the time and effort to get a run going if you can.
Cheers David
On 21 Dec 2011, at 13:36, Jane Song wrote:
Dear Galaxy Expert,
I would like to use Galaxy to de-novo assembly single-end read illumina data (140bp) for plant transcriptomes (without reference). I remember early emails mention trinity in Galaxy. But I could not see at Galaxy web http://main.g2.bx.psu.edu/root . Maybe it is installed in Amarzon EC2? Other suggestions in de-novo assembly plant transcriptomes without reference.
Many thanks and look forward to hearing back from you, Jane
___________________________________________________________ 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:
participants (3)
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David Matthews -
Jane Song -
Jeremy Goecks