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Trinity assembles transcript sequences from Illumina RNA-Seq data.



See versions of trinity which are available:

$module avail trinity


  • 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 --full_cleanup


Notes from the sysadmin during installation:

$ cd /tmp
$ wget "" -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
trinity-software.1438344038.txt.gz · Last modified: 2015/07/31 12:00 by joguya