NAME

       Transdecoder - Transcriptome Protein Prediction

USAGE

       Required:

        -t <string>                            transcripts.fasta

       Common options:

        --retain_long_orfs <int>               retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence
                                                marks it as coding (default: 900 bp => 300aa)

        --retain_pfam_hits <string>                 /path/to/pfam_db.hmm to search
                                               using hmmscan (which should be accessible via your PATH setting)

        --retain_blastp_hits <string>

       Advanced options

        --train <string>                       FASTA file with ORFs to train Markov Mod for protein identification; otherwise
                                               longest non-redundant ORFs used

        -T <int>                               If no --train, top longest ORFs to train Markov Model (hexamer stats) (default: 500)

                                                   2015-12-28                            TRANSDECODER.PREDICT(1)