Bulk RNA-sequencing (RNA-seq) on the NIH Integrated Data Analysis Portal (NIDAP)

This page contains links to recorded video lectures and tutorials that will require approximately 4 hours in total to complete.  You can reach out to us at ncibtep@nih.gov with any questions.  We look forward to seeing you in class and hope you find these materials helpful in better understanding RNA-sequencing and the downstream analysis of RNA-seq workflows on NIDAP.

Please begin with the recorded lecture on the background and methodology of RNA-seq.  Then, follow instructions on how to log-into NIDAP and use the tutorial to guide your own downstream analysis of an RNA-seq training dataset.  At the end of this course, please consider responding to the survey link at the bottom of this page to provide us with feedback and suggestions for improving this course in the future.

If you are returning to NIDAP after having taken the initial training lecture and tutorial and intend to upload your own data for analysis, please watch our Quick Start Guide video for tips on how to get your analysis running quickly.

Troubleshooting Tips:

  • Use only the Chrome web browser to access NIDAP; other browsers (e.g. Safari, Edge, Firefox, etc.) are not supported at this time.
  • To watch videos you must be on VPN or an NIH internal network.
    • You may access NIDAP regardless of VPN status, but the videos linked here are hosted on NIH’s internal video streaming site.

Quick Start Guide: Bulk RNA-seq Analysis on NIDAP

Use this ~20-minute video if you have already watched the lecture and tutorial videos linked below, and would now like a short guide on how to get your own data imported into NIDAP so that you can begin your own analysis. This guide will give you the basics of how to prepare your input files (metadata and raw counts), how to get them into NIDAP, and how to begin a code workbook to analyze them with the same workflow that the tutorials (below) show in detail. In short, the steps to quickly get your dataset into NIDAP and an analysis started are:

  • Prepare raw counts and sample metadata inputs (watch out for restrictions on names)
  • Upload inputs to NIDAP as datasets
  • Begin a new Code Workbook
  • Import the input datasets into your new Code Workbook
  • Add the “CCBR Bulk RNA-seq Workflow” multi-node template
  • Swap the Environment profile from “default” to “bulk-rna-seq”

Background Lecture: Bulk RNA-seq Analysis – Background & Methodology

This lecture video is split into four ~20-minute parts. Together they explain the minimal theoretical background you should need to understand what happened in an RNA-seq experiment before you begin the downstream analysis on NIDAP. This lecture will provide a brief overview of Bulk RNA-seq, and what the upstream and downstream portions of the analysis produce. After absorbing this background information, you are ready to continue your learning with the Guided Tutorial further below.

The topics covered in this Background Lecture are:

  • Introduction to course
  • RNA-seq: Background
  • RNA-seq: Overview of upstream analysis
  • RNA-seq: Overview of downstream analysis
  • Understanding filtering, normalization, and batch correction of RNA-seq data
  • RNA-seq: Experimental design considerations

Guided Tutorial with Training Dataset:  Bulk RNA-seq Analysis on NIDAP

This ~4-hour video is a guided tutorial that will walk you through the details of each step of the downstream analysis of Bulk RNA-seq datasets on NIDAP. To follow-along with these videos, open another tab in your Chrome web browser and log-in to NIDAP using your NIH credentials here:  https://nidap.nih.gov/.

The topics covered in this Guided Tutorial are:

  • How to access NIDAP
  • Orientation to the NIDAP home page
  • Accessing the Bulk RNA-seq training dataset
  • Launching your first code workbook with the training dataset
  • Orientation to the code workbook
  • Understanding the inputs needed to begin your analysis
  • Understanding your metadata
  • Template organization: layout and coloring
  • Filtering out low count genes
  • Normalizing counts
  • Batch correction
  • Making and understanding your first sample-wise heatmap
  • Differential Expression of Genes (DEG) analysis
  • Making and understanding your first Volcano plot
  • Making a Venn diagram of your DE genes across multiple contrasts
  • Preranked Gene Set Enrichment Analysis (GSEA)
  • Visualizing and understanding the results of a GSEA finding

Course Survey:  Bulk RNA-seq Analysis on NIDAP

Please consider taking this short survey to provide us with feedback and suggestions on how to improve this course in the future.