2024 eResearch - Session 6 : Small RNAs: A regulatory network of a broad range of biological processes

Aims

• Learn to process small RNAseq data to identify differentially expressed genes (DEGs) using the nf-core/smrnaseq pipeline (version 2.13.1)

• Run the nextflow nf-core/rnaseq pipeline in the HPC cluster. Exercises include:

  • Human - Huntington Disease:

    • Download public data from the European Nucleotide Archive (ENA) database

    • Running the full nf-core/smrnaseq pipelines using the human reference genome (GRCh38) provided by nf-core (igenomes) and the reference miRBase database

    • Running the full nf-core/smrnaseq pipelines using the human reference genome (GRCh38) provided by nf-core (igenomes) and the reference MirGeneDB database

  • Elucidating the role of the Drosha Proline-Rich Disordered (PRD) domain:

    • We will use a basic-science project to assess how mutants of the PRD domain influence the expression of miRNAs.

Today’s overview

1. Introduction to nf-core/smRNA-seq

2. Preparing working directory

3. Fetch public RNA-seq data

4. Prefrontal cortex - Huntington Disease vs. controls - small RNA-seq pipeline (miRBase)

5. Prefrontal cortex - Huntington Disease vs. controls - small RNA-seq pipeline (MirGeneDB)

6. Drosha’s controls vs Proline-Rich Disorder (PRD) domain mutant

Before we start using the HPC, let’s start an interactive session:

• where:

  • ‘walltime’ is amount of time requested to run the interactive session

  • ‘cpus’ number of CPUs to be used by the interactive session

  • ‘mem’ amount of memory assigned to the interactive session

Reference nf-core/smRNA pipeline: https://nf-co.re/smrnaseq/2.3.1