Trinity assembles transcript sequences from Illumina RNA-Seq data.

• Version: v2.0.6
• Added: March, 2015
• Link: https://trinityrnaseq.github.io

See versions of trinity which are available:

$module avail trinity

Note:

• You should always use the –full_cleanup option so that Trinity can clean up after itself by removing all the intermediary files it has created except for the final Trinity.fasta results file.
• Trinity creates millions of small files – which causes problems on the HPC storage server – so you must direct output from these jobs to /var/scratch instead of your home folder. For example:

#!/bin/env bash
#SBATCH -p highmem
#SBATCH -J trinity
#SBATCH -n 8

module load trinity/v2.0.6
module load bowtie/1.1.1
module load samtools/1.2

# cd to working dir just in case
export WORKDIR=/var/scratch/$USER/$SLURM_JOBID
mkdir -p $WORKDIR
cd $WORKDIR

# match CPUs to amount requested in SBATCH options!
Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 8 --output trinity-fish2

Notes from the sysadmin during installation:

$ cd /tmp
$ wget "https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz" -O trinity-v2.0.6.tar.gz
$ tar -xvf trinity-v2.0.6.tar.gz
$ cd trinityrnaseq-2.0.6/
$ scl enable devtoolset-2 bash
$ CC=clang make
$ CC=clang make plugins
$ sudo mkdir /export/apps/trinity/v2.0.6
$ cp -r * /export/apps/trinity/v2.0.6
$ sudo chown -R root:root /export/apps/trinity/v2.0.6