Trinity
Introduction
Trinity
assembles transcript sequences from Illumina RNA-Seq data.
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