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Question: De Novo Rna-Seq Workflow
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gravatar for Carlos Canchaya
5.2 years ago by
Carlos Canchaya • 10
Carlos Canchaya • 10 wrote:
Hi guys, I am looking for a de novo RNA-seq workflow that uses trinity. Any idea if there is one available? Bests, Carlos Carlos Canchaya ccanchaya@gmail.com
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modified 5.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.2 years ago by Carlos Canchaya • 10
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gravatar for Jennifer Hillman Jackson
5.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Carlos, We don't have a Trinity workflow available and I've looked through all of the donated community tutorials and have not been able to find one there, either. The Tool Shed has a newer feature that permits Workflow sharing, but that also lacks a RNA-seq assembly->analysis workflow. The closest I came was this post, over a year ago to the galaxy-dev@bx.psu.edu mailing list. The general path outlined seems reasonable and is similar to what you would find in the Trinity documentation: http://dev.list.galaxyproject.org/building-a-full-trinity-workflow- from-assembly-through-analysis-td4655675.html Just to let you now, Jeremy (the wrapper author) let me know that the Trinity wrapper in the Tool Shed may be slightly outdated compared to the most recent binaries, so keep this in mind if you decide to use it. Reviewing publications that make use of this tool is probably the best approach. Or you could explore NGS hubs such as seqanswers.com to find out what is available/being discussed. Sorry that we could not help out more with this specific analysis, Best, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENT • link written 5.2 years ago by Jennifer Hillman Jackson ♦ 25k
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