mRNA-Seq BY-COVID Pipeline
Version 1

Workflow Type: Galaxy
Work-in-progress

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

Could not render the workflow diagram.

Inputs

ID Name Description Type
mRNA-Seq Reads n/a Input list of fastqsanger format sequencing data
  • File[]
UCSC Genome n/a Export of UCSC Genome, just the genes.
  • File
factordata n/a 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

Steps

ID Name Description
3 n/a n/a
4 n/a n/a
5 n/a n/a
6 n/a n/a
7 n/a n/a
8 n/a n/a
9 n/a n/a
10 n/a n/a
Gene Lengths n/a n/a
Multi QC raw reads n/a n/a
countdata n/a n/a
annodata n/a n/a
15 n/a n/a
limma DEG analysis n/a n/a
17 n/a n/a
18 n/a n/a
MINERVA Formatting n/a n/a
20 n/a n/a

Outputs

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

Version History

Version 1 (earliest) Created 6th Dec 2023 at 13:38 by Helena Rasche

Added/updated 966 files


Open master 46393c2
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Created: 6th Dec 2023 at 13:38

Last updated: 6th Dec 2023 at 13:47

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