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TRANSDECODER.PREDICT(1) Transcriptome Protein Prediction TRANSDECODER.PREDICT(1)

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>            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_orf                      Retain only the single best ORF per transcript.
                                        (Best is defined as having (optionally pfam and/or blast support) and longest orf)

 --cpu <int>                            Use multiple cores for cd-hit-est. (default=1)

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

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)
                                        Note, 10x this value are first selected for use with cd-hit to remove 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
2016-11-10 3.0.1+dfsg-1