NAME¶

Transdecoder - Transcriptome Protein Prediction

USAGE¶

Required:

 -t <string>                            transcripts.fasta

Common options:

 --retain_long_orfs_mode <string>        'dynamic' or 'strict' (default: dynamic)
                                        In dynamic mode, sets range according to 1%FDR in random sequence of same GC content.
 
 --retain_long_orfs_length <int>         under 'strict' mode, retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence 
                                         marks it as coding (default: 1000000) so essentially turned off by default.)
 --retain_pfam_hits <string>            domain table output file from running hmmscan to search Pfam (see transdecoder.github.io for info)     
                                        Any ORF with a pfam domain hit will be retained in the final output.
 
 --retain_blastp_hits <string>          blastp output in '-outfmt 6' format.
                                        Any ORF with a blast match will be retained in the final output.
 --single_best_only                     Retain only the single best orf per transcript (prioritized by homology then orf length)
 -G <string>                            genetic code (default: universal; see PerlDoc; options: Euplotes, Tetrahymena, Candida, Acetabularia, ...)
 --no_refine_starts                     start refinement identifies potential start codons for 5' partial ORFs using a PWM, process on by default.

Advanced options

 -T <int>                               If no --train, top longest ORFs to train Markov Model (hexamer stats) (default: 500)
                                        Note, 10x this value are first selected for removing redundancies,
                                        and then this -T value of longest ORFs are selected from the non-redundant set.

Genetic Codes¶

See <http://golgi.harvard.edu/biolinks/gencode.html>. These are currently supported:

 universal (default)
 Euplotes
 Tetrahymena
 Candida
 Acetabularia
 Mitochondrial-Canonical
 Mitochondrial-Vertebrates
 Mitochondrial-Arthropods
 Mitochondrial-Echinoderms
 Mitochondrial-Molluscs
 Mitochondrial-Ascidians
 Mitochondrial-Nematodes
 Mitochondrial-Platyhelminths
 Mitochondrial-Yeasts
 Mitochondrial-Euascomycetes
 Mitochondrial-Protozoans