Question: Suggestions For De Novo Assembly Plant Transcriptome Without Reference
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gravatar for Jane Song
6.1 years ago by
Jane Song10
Jane Song10 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 <galaxy-user@bx.psu.edu>
assembly • 1.1k views
ADD COMMENTlink modified 6.1 years ago by David Matthews630 • written 6.1 years ago by Jane Song10
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gravatar for David Matthews
6.1 years ago by
United Kingdom
David Matthews630 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
ADD COMMENTlink written 6.1 years ago by David Matthews630
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.
ADD REPLYlink written 6.1 years ago by Jeremy Goecks2.2k
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