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trinity [2017/10/24 17:52] (current)
jokinsey Create Trinity documentation
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 +====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]].
 +
 +
  
trinity.txt · Last modified: 2017/10/24 17:52 by jokinsey