Gigascience_Fusions_demonstration_STS26T-Gent_Workflow
1.0

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Workflow Type: Galaxy

Create a protein Fusion database through the Arriba workflow

Associated Tutorial

This workflows is part of the tutorial Neoantigen 1: Fusion-Database-Generation, available in the GTN

Features

Thanks to...

Workflow Author(s): GalaxyP

Tutorial Author(s): Subina Mehta, Katherine Do, James Johnson

Tutorial Contributor(s): Pratik Jagtap, Timothy J. Griffin

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1383?version=1

Inputs

ID Name Description Type
RNA-Seq_Reads_1 #main/RNA-Seq_Reads_1 Forward strand
  • File
RNA-Seq_Reads_2 #main/RNA-Seq_Reads_2 Reverse strand
  • File
human_reference_genome.fasta #main/human_reference_genome.fasta Reference HUMAN FASTA
  • File
human_reference_genome_annotation.gtf #main/human_reference_genome_annotation.gtf human GTF
  • File

Steps

ID Name Description
4 Arriba-Get-Filters toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.4.0+galaxy1
5 Uncompressed-RNA-Seq-forward-reads Uncompressed RNA-Seq forward reads CONVERTER_gz_to_uncompressed
6 Uncompressed-RNA-Seq-reverse-reads Uncompressed RNA-Seq reverse reads CONVERTER_gz_to_uncompressed
7 RNA_STAR toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4
8 Arriba toolshed.g2.bx.psu.edu/repos/iuc/arriba/arriba/2.4.0+galaxy1
9 Reformating Fusion data toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
10 Table_generation_from_Fusion_data toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1
11 Converting_Tabular_to_Fasta toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
12 Arriba-Fusion-Database toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3

Outputs

ID Name Description Type
Arriba-Fusion-Database #main/Arriba-Fusion-Database n/a
  • File
Arriba-Fusions-tsv #main/Arriba-Fusions-tsv n/a
  • File
Arriba-Get-Filters_blacklist #main/Arriba-Get-Filters_blacklist n/a
  • File
Arriba-Get-Filters_cytobands #main/Arriba-Get-Filters_cytobands n/a
  • File
Arriba-Get-Filters_known_fusions #main/Arriba-Get-Filters_known_fusions n/a
  • File
Arriba-Get-Filters_protein_domains #main/Arriba-Get-Filters_protein_domains n/a
  • File
Converting_Tabular_to_Fasta #main/Converting_Tabular_to_Fasta n/a
  • File
RNA_STAR_mapped_reads #main/RNA_STAR_mapped_reads n/a
  • File
Reformated_Fusion_data #main/Reformated_Fusion_data n/a
  • File
Table_generation_from_Fusion_data #main/Table_generation_from_Fusion_data n/a
  • File
Uncompressed-RNA-Seq-forward-reads #main/Uncompressed-RNA-Seq-forward-reads n/a
  • File
Uncompressed-RNA-Seq-reverse-reads #main/Uncompressed-RNA-Seq-reverse-reads n/a
  • File

Version History

1.0 (earliest) Created 20th Jan 2025 at 13:07 by Helena Rasche

Added/updated 4 files


Open master 358a385
help Creators and Submitter
Creators
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Submitter
Tool
STAR
License
No license - no permission to use unless the owner grants a licence
Activity

Views: 14   Downloads: 3

Created: 20th Jan 2025 at 13:07

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Total size: 231 KB
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