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