#!/usr/bin/env bash

#PBS -N TransAsmblExercise
#PBS -l nodes=1:ppn=8,walltime=4:00:00,vmem=125gb
#PBS -j oe
#PBS -m abe
#PBS -q shared
#PBS -M your.email@indiana.edu

# Load software
module load java
module load bowtie/1.1.1
module load samtools
module load trinityrnaseq/2014-07-17

WD=/N/dc2/scratch/YourUsername/trans-asmbl
cd $WD

Trinity --seqType fq --JM 100G --CPU 8 --output test-assembly \
        --left  pdom-q1-subsample-1.fq.gz \
        --right pdom-q1-subsample-2.fq.gz