Software: Trinity
Description
Trinity assembles transcript sequences from Illumina RNA-Seq data.
Available Versions
| Unspecified: | 2.12.0 2.13.2 2.14.0 2.15.0 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/trinity and its home page on Github.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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