TRANSDECODER.PREDICT

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