Installing and using EvidentialGene

[Maya Britstein]

Hi all,

a colleague of mine recommended that I use this tool, specifically the script tr2aacbs to improve a transcriptome that I assembled using trinity.

However, I am not a computer/code expert, and I'm having a lot of difficulties in understand how to use this tool.

Can someone help me? or direct me to where are the instructions?

Thanks,

Maya

[Don Gilbert]

Maya,

The instructions for evidentialgene's tr2aacds program, which reduces over-assemblies of RNA-seq to

a sensible non-redundant set of genes with alternates, is here
 http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html

There is however a presumption that you and other users of these tools have a degree of Unix

computing skills. I realize many of those now assembling genes do not, but want a very simple plug and play

choice.  My suggestion is that you ask those who provide the transcript assembly programs you use, e.g.

Trinity, to likewise install and test Evigene tools for  your use, and help as needed with that.

While you are about asking for help with Unix experts to maintain those computers with Trinity gene assembler,

let them know also that other gene assemblers will do a better job than Trinity .. that is part of the reason

for EvidentialGene and its methods, to choose among many gene assemblies for the "just right" gene set.

Other readers here may have better advice for you.

- Don Gilbert

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don gilbert - www.bio.net - bioinformatics - indiana.u.