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 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 --full_cleanup

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