haotu : an open lab notebook


Install Trinity RNA-Seq on Ubuntu

Filed under: De Novo assembly, Genomics, RNAseq — S @ 04:36

I am going to try to install the Trinity RNA-Seq de novo assembler to create contigs of some tadpole RNA-seq data.

1. Download tar ball at sourceforgehttp://sourceforge.net/projects/trinityrnaseq/
2. Then I extracted it to a folder and typed


3. then you can go to the sample data folder and run the example script

sudo ./runMe.sh

This all seemed to work fine on my laptop…

On the Trinity website they refer to left and right reads for paired end files, this corresponded to files 1 and 2, respectively, that I received from BGI.


1 Comment »

  1. Hi, did you ever get Trinity working?

    I have installed Trinity and tested it using the runMe.sh script with the sample data provided…

    But now I am trying to figure out how exactly to run MY data using Trinity.

    Any insights would be appreciated.


    Comment by Thomas — 2011/06/17 @ 11:47

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