Bioinformatics workshop series: 5. Streamlining RNAseq Analysis with the YCGA Pipeline (In-Person)

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Session 5 – Streamlining RNAseq Analysis with the YCGA Pipeline

Registration required* and In-Person

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

Series Details: see below

Summary: In this hands-on workshop, participants will learn how to use the YCGA bulk RNA-seq pipeline to produce count data from fastq files. Since YCGA pipelines have similar user interfaces the knowledge learned can be applied to other pipelines and tools that YCGA offers. We will review some of them.

You will learn how to:

• Use some of the NGS tools offered by the YCGA Bioinformatics Group
• Run the Bulk-RNAseq YCGA pipeline

Requirements:

• Have participated in session 3 and are familiar with bash/CLI or Jupyter Notebooks
• 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, intermediate, and Advanced 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 own analysis.

Date: Every Tuesday from February 6 until March 26

Time: from 10am-12pm

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.

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