Description

TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file.

Input

name:type
description
pattern

meta

:map

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

fasta

:file

fasta file

*.{fasta}

Output

name:type
description
pattern

pep

meta

:map

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

${output_dir_name}/*.pep

:file

all ORFs meeting the minimum length criteria, regardless of coding potential. file

*.{pep}

gff3

meta

:map

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

${output_dir_name}/*.gff3

:file

positions of all ORFs as found in the target transcripts. file

*.{gff3}

cds

meta

:map

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

${output_dir_name}/*.cds

:file

the nucleotide coding sequence for all detected ORFs. file

*{cds}

dat

meta

:map

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

${output_dir_name}/*.dat

:file

nucleotide frequencies

*{dat}

folder

${output_dir_name}

:directory

contains all the files from the run

versions_transdecoder

${task.process}

:string

The name of the process

transdecoder

:string

The name of the tool

TransDecoder.LongOrfs --version | sed 's/TransDecoder.LongOrfs //'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

transdecoder

:string

The name of the tool

TransDecoder.LongOrfs --version | sed 's/TransDecoder.LongOrfs //'

:eval

The expression to obtain the version of the tool

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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