1 Short Read Alignment and Quality Control

Introduction to the dataset used in this part of the course

I’ll be using ChIP-seq and RNA-seq datasets to demonstrate how to align ChIP-seq and RNA-seq data to the GRCh38 reference genome.GRCh38/hg38 is the assembly of the human genome released December of 2013, that uses alternate or ALT contigs to represent common complex variation, including HLA loci.