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Trinity assembles transcript sequences from Illumina RNA-Seq data.



See versions of trinity which are available

module avail trinity

Note: 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

# 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 "" -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.1427216662.txt.gz · Last modified: 2015/03/24 17:04 by aorth