mRNA-Seq BY-COVID Pipeline: Analysis
Version 1

Visit source Download RO Crate
Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/948?version=1

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 (earliest) Created 22nd Apr 2024 at 11:09 by Helena Rasche

Added/updated 3 files


Open master 9d4d69f
help Creators and Submitter
Creators
  • Iacopo Cristoferi
  • Helena Rasche
Additional credit

Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center

Submitter
Tools
annotatemyids
limma
GOseq
License
GNU General Public License v3.0 or later
Activity

Views: 32

Created: 22nd Apr 2024 at 11:08

Last updated: 22nd Apr 2024 at 11:09

help Attributions

None

Total size: 36.8 KB
Powered by
 (v.1.15.0-pre)
About Dev WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH