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Trinity assembles transcript sequences from Illumina RNA-Seq data.



See versions of trinity which are available:

$ module avail trinity

Load one version into your environment and run it:

$ module load trinity/v2.11.0
$ Trinity

Notes about running Trinity:

  • Please 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 fasta results
  • Trinity creates millions of small files, which is inefficient and causes problems on the HPC storage server, so you please direct the output from these jobs to a directory inside /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/v2.6.6
    # 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
$ tar xf trinityrnaseq-v2.11.0.FULL.tar.gz
$ cd trinityrnaseq-v2.11.0
$ sed -i 's/cmake/cmake3/' Chrysalis/Makefile Inchworm/Makefile
$ make
$ make plugins
$ sudo yum install python36-numpy.x86_64
$ sudo mkdir -p /export/apps/trinity/v2.11.0
$ sudo cp -r . /export/apps/trinity/v2.11.0
$ export TRINITY_HOME=/export/apps/trinity/v2.11.0
$ module load samtools/1.9 salmon/1.3.0 bowtie2/ jellyfish/2.3.0
$ cd sample_data/test_Trinity_Assembly
$ ./

Consult the installing Trinity guide in the documentation.

trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth