transdecoder
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
Link to section 'Versions' of 'transdecoder' Versions
- 5.5.0
Link to section 'Commands' of 'transdecoder' 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
Link to section 'Module' of 'transdecoder' Module
You can load the modules by:
module load biocontainers
module load transdecoder
Link to section 'Example job' of 'transdecoder' Example job
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