Development and comparison of RNA-Sequencing pipelines for more accurate SNP identification: Practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle

Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy for identifying genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study determined an optimized pipeline for variant detection using a dataset with multiple samples and tissues.