mRNA-Seq BY-COVID Pipeline: Analysis
Version 1

Workflow Type: Galaxy
Work-in-progress

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

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

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

Initial commit


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

Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center

Submitter
Activity

Views: 1003

Created: 19th Dec 2023 at 10:10

help Tags
help Attributions

None

Total size: 2.91 MB
Powered by
(v.1.14.1)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH