Description

TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fasta{:bash}

:file

fasta file

*.{fasta}

fold{:bash}

:directory

Output from the module transdecoder_longorf

*

Output

name:type
description
pattern

pep{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.transdecoder.pep{:bash}

:file

All ORFs meeting the minimum length criteria, regardless of coding potential

*.{pep}

gff3{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.transdecoder.gff3{:bash}

:file

Positions of all ORFs as found in the target transcripts

*.{gff3}

cds{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.transdecoder.cds{:bash}

:file

the nucleotide coding sequence for all detected ORFs

*{cds}

bed{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.transdecoder.bed{:bash}

:file

bed file

*{bed}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

transdecoder
Broad Institute

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

github.com/TransDecoder github.com/TransDecoder/TransDecoder/wiki https://github.com/TransDecoder/TransDecoder
maintainer
Github user Danilo2771
get in touch
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