Trinity

Introduction

Trinity assembles transcript sequences from Illumina RNA-Seq data.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/trinity
Home page: https://github.com/trinityrnaseq/trinityrnaseq/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.12.0, 2.13.2, 2.14.0, 2.15.0

BELL

2.12.0, 2.13.2, 2.14.0, 2.15.0

GAUTSCHI

2.12.0, 2.13.2, 2.14.0, 2.15.0

NEGISHI

2.12.0, 2.13.2, 2.14.0, 2.15.0

SCHOLAR

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 -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers trinity

# Your trinity workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers trinity

# Your trinity workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers trinity

# Your trinity workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers trinity

# Your trinity workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers trinity

# Your trinity workflow...