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

5.5.0

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

You can load the modules by:

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: