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.
TransDecoder identifies likely coding sequences based on the following criteria:
a minimum length open reading frame (ORF) is found in a transcript sequence
a log-likelihood score similar to what is computed by the GeneID software is > 0.
the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 2 forward reading frames.
if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc).
a PSSM is built/trained/used to refine the start codon prediction.
optional the putative peptide has a match to a Pfam domain above the noise cutoff score.
Detailed usage can be found here: https://github.com/TransDecoder/TransDecoder/wiki#running-transdecoder
Versions
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 our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#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
ml biocontainers transdecoder
gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta
gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3
TransDecoder.LongOrfs -t transcripts.fasta
TransDecoder.Predict -t transcripts.fasta