Next Generation Sequencing Data Analysis
This workshop will introduce the basics of next generation sequencing (NGS) data analysis. We will introduce NGS methods and platforms, bioinformatics tools and standards, and data analysis workflows, specifically for DNA-seq (variant analysis) and RNA-seq (transcriptome analysis). The lectures will introduce common software libraries and algorithms used in the bioinformatics community. During the hands-on training sessions, we will perform alignment and analysis of NGS data from scratch using standard software libraries and pipelines.
Completion of any of the above courses and workshops or experience with R is expected. Basic computing skills; a background in Linux and bash scripting is not required though preferred.
The workshop will:
- start with a general introduction to working in a linux environment and running command-line tools. We will learn the common file formats: fasta, fastq, SAM, BAM, VCF, GTF
- walk through:
- DNA-Seq variant calling analysis
- RNA-Seq analysis with downstream analysis in R
- touch on data retrieval and best practices for making your analysis readable and reproducible.