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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 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:
    #!/usr/bin/env bash
    #SBATCH -p highmem
    #SBATCH -J trinity
    #SBATCH -n 8
    module load trinity/v2.4.0
    # create and change to a working directory on the compute node
    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
$ unzip
$ cd trinityrnaseq-Trinity-v2.4.0
$ scl enable devtoolset-4 bash
$ make
$ make plugins
$ sudo mkdir /export/apps/trinity/v2.4.0
$ make test_trinity
$ sudo cp -r . /export/apps/trinity/v2.4.0
trinity-software.1503404455.txt.gz · Last modified: 2017/08/22 12:20 by aorth