Extract transcripts - TSI
Version 1

Workflow Type: Galaxy

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

Repeat masking
RNAseq QC and read trimming
Find transcripts
Combine transcripts
Extract transcripts
Convert formats
Fgenesh annotation

About this workflow:

Input: merged_transcriptomes.fasta.
Runs TransDecoder to produce longest_transcripts.fasta
(Runs both the LongOrfs and Predict parts together. Default settings except Long Orfs options: -m =20)
Runs Busco on output.

SEEK ID: https://workflowhub.eu/workflows/879?version=1

DOI: 10.48546/workflowhub.workflow.879.1

Inputs

ID	Name	Description	Type
merged_transcriptomes.fasta	#main/merged_transcriptomes.fasta	n/a	File

Steps

ID	Name	Description
1	Text transformation	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1
2	TransDecoder	toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/5.5.0+galaxy2
3	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0

Outputs

ID	Name	Description	Type
busco_sum	#main/busco_sum	n/a	File
busco_table	#main/busco_table	n/a	File
out_bed	#main/out_bed	n/a	File
out_cds	#main/out_cds	n/a	File
out_gff3	#main/out_gff3	n/a	File
out_lo_cds	#main/out_lo_cds	n/a	File
out_lo_pep	#main/out_lo_pep	n/a	File
out_pep	#main/out_pep	n/a	File