Trinity#

Introduction#

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Versions#

2.15.0
2.15.1

Commands#

abundance_estimates_to_matrix.pl
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
Trinity
Trinity_gene_splice_modeler.py
TrinityStats.pl
wgsim
wgsim_eval.pl
zoom2sam.pl

Example job#

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=trinity     # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load trinity/XXXX       ### Latest version is recommended.