mRNA-Seq BY-COVID Pipeline: Analysis
Version 1

Workflow Type: Galaxy

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


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
4 Extract dataset __EXTRACT_DATASET__
5 countdata
6 annodata
7 Replace Text
8 limma DEG analysis
9 Extract dataset __EXTRACT_DATASET__
10 MINERVA Formatting Cut1
11 Join two Datasets join1
12 Compute
13 Cut Cut1
14 Unique
15 Cut Cut1
16 Cut Cut1
17 goseq


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

Version 1 (earliest) Created 19th Dec 2023 at 10:10 by Helena Rasche

Initial commit

Frozen Version-1 b946ad9
help Creators and Submitter
  • Iacopo Cristoferi
  • Helena Rasche
Additional credit

Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center


Views: 1003

Created: 19th Dec 2023 at 10:10

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Total size: 2.91 MB
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