mRNA-Seq BY-COVID Pipeline: Analysis
1.0

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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 mRNA-Seq BY-COVID Pipeline: Analysis, available in the GTN

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

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

Funder(s): BeYond-COVID

SEEK ID: https://dev.workflowhub.eu/workflows/1332?version=1

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[]

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