====Trinity====

Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity was developed at the [[https://www.broadinstitute.org|Broad Institute]] and the [[http://www.cs.huji.ac.il/|Hebrew University of Jerusalem]]. You can find more information on Trinity [[https://github.com/trinityrnaseq/trinityrnaseq/wiki|here]].

====Environment Setup====

Edit your ''$HOME/.bashrc'' file to contain the line of code below which will include the dependency for Trinity. You will have to log back in for this to take effect.

<code>
module load trinity/2.3.2
</code>

In your ''$HOME'' directory create a directory called ''TRINITY-JOBS'' to store the files we will be using. Copy the testing files created be Trinity into the new directory.

<code>
razor-l1:jokinsey:~$ mkdir TRINITY-JOBS
razor-l1:jokinsey:~$ cp /share/apps/trinity/trinityrnaseq-2.3.2/sample_data/test_Trinity_Assembly/reads.left.fq.gz ./TRINITY-JOBS/
razor-l1:jokinsey:~$ cp /share/apps/trinity/trinityrnaseq-2.3.2/sample_data/test_Trinity_Assembly/reads.right.fq.gz ./TRINITY-JOBS/
</code>

====Example Job====

Now inside the new directory create a ''PBS'' script named ''trinity.pbs'' to run the job, that contains the information below.

<code>
#!/bin/bash
#PBS -N trinity
#PBS -q tiny12core
#PBS -j oe
#PBS -o trinity.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=1:00:00

cd $PBS_O_WORKDIR
mkdir trinity.$PBS_JOBID
cp reads.right.fq reads.left.fq /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

Trinity --seqType fq --left reads.left.fq --right reads.right.fq --CPU $PBS_NUM_PPN --max_memory 8G --output $PBS_O_WORKDIR/trinity.$PBS_JOBID
</code>

All thats left is to submit the job.

<code>
razor-l1:jokinsey:~/TRINITY-JOBS$ qsub trinity.pbs
</code>

The output of this job will be located in a new directory ''trinity.$PBS_JOBID'' created where the job is run from. There will be a lot of files in this output directory, and a good starting file to look at is the ''Trinity.fasta'' file. More information on the output is located [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Output-of-Trinity-Assembly|here]].