lncRNAs-annotation/main
v0.1

Workflow Type: Galaxy

This workflow runs the FEELnc tool to annotate long non-coding RNAs. Before annotating these long non-coding RNAs, StringTie will be used to assemble the RNA-seq alignments into potential trancriptions. The gffread tool provides a genome annotation file in GTF format.

SEEK ID: https://workflowhub.eu/workflows/1324?version=1

Inputs

ID	Name	Description	Type
Alignments from RNA-seq	#main/Alignments from RNA-seq	Alignments from RNA-seq	File
Genome annotation	#main/Genome annotation	Genome annotation	File
Genome assembly	#main/Genome assembly	Genome assembly	File
strandedness	#main/strandedness	strandednes	string

Steps

ID	Name	Description
4	Map parameter value	Map parameter value toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
5	gffread	Protein sequences extracted from genomic annotation toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0
6	Assembly step with StringTie	StringTie is a fast, highly efficient assembler of RNA-Seq alignments into potential transcripts. toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0
7	lncRNA annotation step with FEELnc	The FEELnc pipeline identifies and classifies long non-coding RNAs (lncRNAs) through three main steps: filter, codpot and classifier. toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2.1+galaxy0
8	Concatenation step	The lncRNA annotation is merged with the reference annotation to create a unified genome annotation containing both mRNAs and lncRNAs. cat1

Outputs

ID	Name	Description	Type
annotation	#main/annotation	n/a	File
annotation final	#main/annotation final	n/a	File
candidate lncRNA	#main/candidate lncRNA	n/a	File
candidate mRNA	#main/candidate mRNA	n/a	File
classification	#main/classification	n/a	File
stringtie gtf	#main/stringtie gtf	n/a	File