TRANSDECODER.PREDICT(1)

NAME
TransDecoder.Predict - predicts the likely coding regions among the ORFs

DESCRIPTION
######################################################################################## # ______ ___ __ # /_ __/______ ____ ___ / _ \___ _______ ___/ /__ ____ # / / / __/ _ `/ _\(_-</ // / -_) __/ _ \/ _ / -_) __/ # /_/ /_/ \_,_/_//_/___/____/\__/\__/\___/\_,_/\__/_/ .Predict # ######################################################################################## # # Transdecoder.LongOrfs|http://transdecoder.github.io> - Transcriptome Protein Prediction # # # 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) # # --output_dir | -O <string> same output directory from the TransDecoder.LongOrfs # # --no_refine_starts start refinement identifies potential start codons for 5' partial ORFs using a PWM, process on by default. # ## Advanced options # # -T <int> 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_code | -G <string> genetic code (default: universal; see PerlDoc; options: Euplotes, Tetrahymena, Candida, Acetabularia, ...) # Genetic Codes (derived from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) Acetabularia Candida Ciliate Dasycladacean Euplotid Hexamita Mesodinium Mitochondrial-Ascidian Mitochondrial-Chlorophycean Mitochondrial-Echinoderm Mitochondrial-Flatworm Mitochondrial-Invertebrates Mitochondrial-Protozoan Mitochondrial-Pterobranchia Mitochondrial-Scenedesmus_obliquus Mitochondrial-Thraustochytrium Mitochondrial-Trematode Mitochondrial-Vertebrates Mitochondrial-Yeast Pachysolen_tannophilus Peritrich SR1_Gracilibacteria Tetrahymena Universal # # #########################################################################################