Bioinformatics workshop series: 4. RNAseq Data Processing: A Step-by-Step Guide from raw sequences to counts. (In-Person)

Registration is required. Click here to register.

Session 4 – RNAseq Data Processing: A Step-by-Step Guide from raw sequences to counts.

Presenter: Dr. Francesc Lopez-Giraldez, Yale Center for Genomic Analysis

Series Details: see below

Summary: Learn the detailed process of transforming raw RNAseq data (fastq format) into meaningful raw counts, without relying on automated pipelines. This hands-on workshop emphasizes the step-by-step methodology for data processing and analysis. For this hands-on workshop, participants will be using Open OnDemand and Jupyter Notebooks.

You will learn how to:

• QC, filter, and trim NGS sequences
• Align sequences to a reference genome
• Produce a count matrix ready to be used with DESeq2

Requirements:

• Have participated in session 3 or become familiar with bash/CLI or Jupyter Notebook
• Bring a laptop.
• HPC account to access Yale Open OnDemand, if you don't have an account bring your laptop with R and RStudio installed.

This session is suitable for both beginner and intermediate users.

Bioinformatics workshop series: Intro to bulk RNA-seq data analysis: from experimental design to pathway analysis.

GENERAL DESCRIPTION: This workshop series offers an introduction to bulk RNA-seq data analysis, guiding participants through each step, from library preparation to gene set enrichment analysis. The series is composed of 8 sessions (see table below). The sessions will be led by field experts from the Yale Centers for Genomic Analysis (YCGA), Computational Research (YCRC), and Cushing/Whitney Medical Library Bioinformatics Support Hub to better connect you with bioinformatics services available at Yale.

We have structured this series in such a manner as to provide practical skills in experimental design, data processing, and functional analysis. The series is ideal for those new to the field of transcriptomics or those wanting to start performing their analysis.

Date: Every Tuesday from February 6 until March 26

Time: from 10 am-12 pm

Requirements: No previous command line experience required.

Seating Information: For registered participants, seating operates on a first-come, first-served basis. Please ensure timely arrival to secure your seat.

*Registrations for March sessions will open at the end of February.

2/06/24

Session 1 - Foundations of Bulk-RNAseq Library Preparation

In-person

Bony De Kumar, PhD

2/13/24

Session 2 - Considerations for Designing Next-Generation Sequencing Experiments

In-person

Francesc Lopez Giraldez, PhD

2/20/24

Session 3 - Introduction to the Yale Clusters and Open OnDemand

In-person

Robert Bjornson, PhD

2/27/24

Session 4 - RNAseq Data Processing: A Step-by-Step Guide from raw sequences to counts

In-person

Francesc Lopez Giraldez, PhD

3/05/24

Session 5 – Streamlining RNAseq Analysis with the YCGA Pipeline

In-person

Francesc Lopez Giraldez, PhD

3/12/24

Session 6 – Analysis of differential gene expression of bulk RNA-seq data using “DESeq2” in RStudio.

In-person

Sofia Fertuzinhos, PhD

3/19/24

Session 7 - Functional analysis using R

In-person

Bony De Kumar, PhD

3/26/24

Session 8 - Functional analysis using Gene Set Enrichment Analysis (GSEA)

In-person

Rolando Milian, MLS