Trinity

Introduction

Trinity assembles transcript sequences from Illumina RNA-Seq data.

For more information, please check its website: https://biocontainers.pro/tools/trinity and its home page on Github.

Versions

  • 2.12.0

  • 2.13.2

  • 2.14.0

  • 2.15.0

Commands

  • Trinity

  • TrinityStats.pl

  • Trinity_gene_splice_modeler.py

  • ace2sam

  • align_and_estimate_abundance.pl

  • analyze_blastPlus_topHit_coverage.pl

  • analyze_diff_expr.pl

  • blast2sam.pl

  • bowtie

  • bowtie2

  • bowtie2-build

  • bowtie2-inspect

  • bowtie2sam.pl

  • contig_ExN50_statistic.pl

  • define_clusters_by_cutting_tree.pl

  • export2sam.pl

  • extract_supertranscript_from_reference.py

  • filter_low_expr_transcripts.pl

  • get_Trinity_gene_to_trans_map.pl

  • insilico_read_normalization.pl

  • interpolate_sam.pl

  • jellyfish

  • novo2sam.pl

  • retrieve_sequences_from_fasta.pl

  • run_DE_analysis.pl

  • sam2vcf.pl

  • samtools

  • samtools.pl

  • seq_cache_populate.pl

  • seqtk-trinity

  • sift_bam_max_cov.pl

  • soap2sam.pl

  • tabix

  • trimmomatic

  • wgsim

  • wgsim_eval.pl

  • zoom2sam.pl

Module

You can load the modules by:

module load biocontainers
module load trinity

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Trinity on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 6
#SBATCH --job-name=trinity
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers trinity

Trinity --seqType fq --left reads_1.fq --right reads_2.fq \
    --CPU 6 --max_memory 20G