Transdecoder

Introduction

Transdecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/transdecoder

Home page: https://github.com/TransDecoder/TransDecoder

Note

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

Versions

Cluster	Version(s)
ANVIL	5.5.0
BELL	5.5.0
GAUTSCHI	5.5.0
NEGISHI	5.5.0
SCHOLAR	5.5.0

Commands

• TransDecoder.LongOrfs

• TransDecoder.Predict

• cdna_alignment_orf_to_genome_orf.pl

• compute_base_probs.pl

• exclude_similar_proteins.pl

• fasta_prot_checker.pl

• ffindex_resume.pl

• gene_list_to_gff.pl

• get_FL_accs.pl

• get_longest_ORF_per_transcript.pl

• get_top_longest_fasta_entries.pl

• gff3_file_to_bed.pl

• gff3_file_to_proteins.pl

• gff3_gene_to_gtf_format.pl

• gtf_genome_to_cdna_fasta.pl

• gtf_to_alignment_gff3.pl

• gtf_to_bed.pl

• nr_ORFs_gff3.pl

• pfam_runner.pl

• refine_gff3_group_iso_strip_utrs.pl

• refine_hexamer_scores.pl

• remove_eclipsed_ORFs.pl

• score_CDS_likelihood_all_6_frames.pl

• select_best_ORFs_per_transcript.pl

• seq_n_baseprobs_to_loglikelihood_vals.pl

• start_codon_refinement.pl

• train_start_PWM.pl

• uri_unescape.pl

Module

You can load the modules by:

module load biocontainers
module load transdecoder

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 transdecoder on our clusters:

Anvil

#!/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=transdecoder
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers transdecoder

# Your transdecoder workflow...

Bell, Gautschi, or Negishi

#!/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=transdecoder
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers transdecoder

# Your transdecoder workflow...

Gautschi-AI

#!/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=transdecoder
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers transdecoder

# Your transdecoder workflow...

Gilbreth

#!/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=transdecoder
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers transdecoder

# Your transdecoder workflow...

Scholar

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

module --force purge
module biocontainers transdecoder

# Your transdecoder workflow...