mRNA-Seq BY-COVID Pipeline: Analysis
1.0

Workflow Type: Galaxy

Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA

Associated Tutorial

This workflows is part of the tutorial Pathway analysis with the MINERVA Platform, available in the GTN

Features

Thanks to...

Workflow Author(s): Iacopo Cristoferi, Helena Rasche, Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center

Tutorial Author(s): Marek Ostaszewski, Matti Hoch, Iacopo Cristoferi, Myrthe van Baardwijk, Saskia Hiltemann, Helena Rasche

Tutorial Contributor(s): Helena Rasche, Matti Hoch, Mira Kuntz, José Manuel Domínguez, Sanjay Kumar Srikakulam, Björn Grüning, Linelle Abueg, Saskia Hiltemann

Grants(s): BeYond-COVID

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
factordata factordata A two column factor table with (Sample Identifier, Condition) This workflow assumes a 1 factor, 2 level analysis, and was specifically designed around SARS-CoV-2 analysis with two levels, e.g. ``` SampleName Group SRR16683284 COVID SRR16683283 COVID SRR16683271 healthy SRR16683270 healthy ```
  • File
featureCounts: Counts featureCounts: Counts count data collection with two column datasets (gene_id, count)
  • File[]
featureCounts: Lengths featureCounts: Lengths featureCounts Lengths collection
  • File[]

Steps

ID Name Description
3 Column join toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
4 Extract dataset __EXTRACT_DATASET__
5 countdata toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
6 annodata toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1
7 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
8 limma DEG analysis toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0
9 Extract dataset __EXTRACT_DATASET__
10 MINERVA Formatting Cut1
11 Join two Datasets join1
12 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.4
13 Cut Cut1
14 Unique toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0
15 Cut Cut1
16 Cut Cut1
17 goseq toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0

Outputs

ID Name Description Type
count_data count_data n/a
  • File
limma_report limma_report n/a
  • File
minerva_table minerva_table n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 11:04 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 11:04

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