.. _backbone-label:

##############
 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.

**********
 Versions
**********

-  5.5.0
-  5.7.1

**********
 Commands
**********

-  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
-  TransDecoder.LongOrfs
-  TransDecoder.Predict
-  uri_unescape.pl

*************
 Example job
*************

Adjust slurm options based on job requirements (`slurm cheat sheet
<https://slurm.schedmd.com/pdfs/summary.pdf>`_):

.. code::

   #!/bin/bash
   #SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
   #SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
   #SBATCH -N 1   # Number of nodes
   #SBATCH -n 1   # Number of tasks per node
   #SBATCH -c 4   # Number of CPU cores per task
   #SBATCH --mem=8G       # Memory required per node
   #SBATCH --job-name=transdecoder        # Job name
   #SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
   #SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
   #SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
   #SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

   module purge   ### Optional, but highly recommended.
   module load transdecoder/XXXX  ### Latest version is recommended.