TrinityRNASeq Guide

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Trinity is a program for de-novo assembly of RNA-Seq transcripts from Illumina.

Check Module Availability

To see which Trinity modules are available to the system, use the following command:

$ module avail trinityrnaseq

You should see all available modules in trinityrnaseq/<version> format:

----------------------- /apps2/Modules/3.2.6/modulefiles -----------------------
trinityrnaseq/2014.04.13p1 trinityrnaseq/v2.0.2-2015

If the module list is empty please contact your administrators.

Loading a Trinity Module

Because Triniy needs gcc to work you will need to load gcc before you load the Trinity module.

You can load the default Trinity module as follows:

$ module load gcc/4.7.1 trinityrnaseq

To see which version is being used, do the following:

$ which Trinity

If your program needs a specific version e.g., trinityrnaseq/2014.04.13p1, do the following:

$ module load gcc/4.7.1 trinityrnaseq/2014.04.13p1

After you load a module you can use it until you log out; you will need to load it again the next time you log in and run your program.

Automatically Loading a Trinity Module

If you frequently use a particular module (which is usual) you can do the following:

$ module initadd gcc/4.7.1 trinityrnaseq

Or, if you need a specific version,

$ module initadd gcc/4.7.1 trinityrnaseq/2014.04.13p1

Note that this auto-loading of the module will start from your next login session. Therefore if you need the module at the present session you will need to load the module using the module load command.

Unloading the Trinity Module

You can unload an already-loaded module as follows:

$ module unload trinityrnaseq

Or, to unload a specific version,

$ module unload trinityrnaseq/2014.04.13p1

To make sure that a module is unloaded, use the command which Trinity which should say /usr/bin/which: no Trinity in ...

Running Trinity

After loading the module you can run Trinity as follows:

$ Trinity <options>