This workshop will include “Connecting and properly using a cloud computing cluster”
Monday August 30 2021: from 10am to 3pm EDT
High-throughput sequencing of RNA libraries (RNA-seq) has become increasingly common and largely supplanted gene microarrays for transcriptome profiling. When processed appropriately, RNA-seq data has the potential to provide a considerably more detailed view of the transcriptome. The CBW has developed a 3-day course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. The tutorials are designed as self-contained units that include example data (Illumina paired-end RNA-seq data) and detailed instructions for installation of all required bioinformatics tools (HISAT, StringTie, etc.).
Participants will gain practical experience and skills to be able to:
- Perform command-line Linux based analysis on the cloud (Amazon AWS)
- Perform basic bioinformatics tasks such as tool installation
- Assess quality of RNA-seq data and perform trimming
- Align RNA-seq data to a reference genome
- Visualize RNA-seq alignments and variants
- Estimate known gene and transcript expression using multiple approaches
- Perform differential expression analysis
- Visualize and summarize the output of RNA-seq analyses in R
- Perform batch correction
- Perform pathway analysis
- Alignment free expression estimation
Graduates, postgraduates, and PIs working or about to embark on an analysis of RNA-seq data. Attendees may be familiar with some aspect of RNA-seq analysis (e.g. gene expression analysis) or have no direct experience.
Prerequisites: Basic familiarity with Linux environment and S, R, or Matlab.
You will also require your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 2GB RAM, 10GB free disk space, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements). If you do not have access to your own computer, you may loan one from the CBW. Please contact firstname.lastname@example.org for more information.
This workshop requires participants to complete pre-workshop tasks and readings.