table of contents
TRANSDECODER.PREDICT(1) | Transcriptome Protein Prediction | TRANSDECODER.PREDICT(1) |
NAME¶
Transdecoder - Transcriptome Protein PredictionUSAGE¶
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 |