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Bioinformatics for Beginners: RNA-Seq

Course Description:

This course was designed to teach the basic skills needed for bioinformatics, including working on the Unix command line. This course primarily focuses on RNA-Seq analysis. All steps of the RNA-Seq workflow, from raw data to differential expression and gene ontology analysis, are covered. However, many of the skills learned are foundational to most bioinformatics analyses and can be applied to the analysis of other types of next generation sequencing experiments.

This course is divided into three modules.

Module 1: Unix and Biowulf (Sep 27th - Oct 18th, 2022)

Lessons focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading data from NCBI.

  • Lesson 1 - Introduction to Unix and the Shell (Recording)
  • Lesson 2 - Navigating file systems with unix (Recording)
  • Lesson 3 - Introduction to Biowulf (Recording)
  • Lesson 4 - Useful Unix (Recording)
  • Lesson 5 - Working on Biowulf (Recording)
  • Lesson 6 - sra-tools, e-utilities, parallel (Recording)
  • Lesson 7 - Review; Downloading RNA-Seq Data (Recording)

Module 2: RNA-Seq Analysis (Oct 20th - Nov 29th, 2022)

Lessons focus on RNA-Seq analysis including experimental design and best practices, quality control, trimming, alignment based methods, classification based methods, feature counts, and differential expression analysis.

  • Lesson 8: Introduction to RNA-Seq (Recording)
  • Lesson 9: Introduction to the data (HBR, UHR) (Recording)
  • Lesson 10: NGS quality check (Recording)
  • Lesson 11: Quality and adapter trimming (Recording)
  • Lesson 12: Review (Recording)
  • Lesson 13: Alignment based RNA-Seq, part 1 (Recording)
  • Lesson 13: Alignment based RNA-Seq, part 2 (Recording)
  • Lesson 14: IGV (Recording)
  • Lesson 15: Differential Expression Analysis (Recording)
  • Lesson 16: Classification based RNA-Seq (Recording)

Module 3: Gene Ontology and Pathway Analysis (Dec 1st - Dec 13th, 2022)

Lessons focus on gene ontology and pathway analysis.

  • Lesson 17: Introduction to gene ontology and pathway analysis (Recording)
  • Lesson 18: Functional enrichment with DAVID
  • Lesson 19: Pathway analysis with Qiagen IPA
  • Lesson 20: Review and Course Wrap-up

Course requirements:

Who can take this course?

There are no prerequisites to take this course. This course is open to NCI-CCR researchers interested in learning bioinformatics skills, especially those relevant to analyzing bulk RNA sequencing data.

What materials are needed to take this course?

To participate in this course, you will need a computer, a reliable internet connection, and a web browser. All classes and help sessions will be held virtually through Webex.  In addition, this class will be taught with the GOLD learning environment on the DNAnexus platform. Learners will need to sign up for a DNAnexus account and complete the registration survey to participate. Class registrants will receive a license to the Biostar Handbook.


Lesson content and practice questions can be found in these pages. Email ncibtep@nih.gov if you have any comments, questions, or concerns.