NAME

       Transdecoder.LongOrfs - Transcriptome Protein Prediction

USAGE

       Required:

        -t <string>                            transcripts.fasta

       Optional:

        --gene_trans_map <string>              gene-to-transcript identifier mapping file (tab-delimited, gene_id<tab>trans_id<return> )

        -m <int>                               minimum protein length (default: 100)

        -G <string>                            genetic code (default: universal; see PerlDoc; options: Euplotes, Tetrahymena, Candida, Acetabularia)

        -S                                     strand-specific (only analyzes top strand)

        -p <int>                               shorten potential 5' partials if they are this percentage of the original protein or longer.

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