Genotyping-by-RNA-Sequencing Tutorial

This is a tutorial for the Genotyping-by-RNA-Sequencing (GBRS) suite of tools. These tools perform several tasks to assist with aligning RNA-Seq reads to genomes which differ from the reference. More specifically, GBRS is designed to align reads to multi-founder crosses between model organisms. This tutorial focuses on mouse genomes, which are well annotated.

Broadly, these tasks are:

1. Insert SNPs and Indels into the reference genome for each strain of interest (i.e. founder strains of a cross) to create imputed genomes;
2. Create strain-specific transcriptomes from the imputed genomes;
3. Align RNS-Seq reads to all of the founder strain genomes;
4. Perform haplotype reconstruction in the cross using genetic variants in the reads;
5. Estimate allele-specific gene and transcript abundance.