Error when running DeSeq2: help resources and input strategies

[jennaj]

Hi @Ketan_Chandra Glad you have this working!

For others reading:

This is the toggle on the form to set which way you want to organize the inputs. Toggle your choice to fit the data you have.

Select datasets per level

1. individual count files (separate files)

   • Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics

2. multiple collections of count files (one collection per factor level)

   • Hands-on: Differential abundance testing of small RNAs / Differential abundance testing of small RNAs / Transcriptomics
   • Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics
   • Hands-on: Whole transcriptome analysis of Arabidopsis thaliana / Whole transcriptome analysis of Arabidopsis thaliana / Transcriptomics
   • Hands-on: De novo transcriptome reconstruction with RNA-Seq / De novo transcriptome reconstruction with RNA-Seq / Transcriptomics

Select group tags corresponding to levels

3. all the count files together in a single collection that is annotated with “group tags”.

   • Hands-on: Group tags for complex experimental designs / Group tags for complex experimental designs / Using Galaxy and Managing your Data

Adding group tags is commonly done at the very start when loading up data, and is a somewhat advanced way to use Galaxy. The bonus is that it means you can process everything together as a batch for upstream steps, but still be able to split out the data when using a downstream tool. The tutorial aboves shows how this works with DESeq2 specifically, but this short guide covers the basics → FAQ: Adding a tag

Many ways to do the same things!