In the past, identifying a gene of interest for a mutant phenotype in maize has proven to be a laborious process. Now, with the aid of next generation sequencing technology, the researcher can quickly identify the region containing a mutant gene and in some cases identify the causative lesion. In our BSA-seq protocol, we use the Galaxy platform for file processing and manipulation. This platform is intended to provide a user friendly experience, so that researchers of any level can clone maize genes. We start with raw sequencing reads from our F2 mapping population and end with plots of SNPs on each chromosome and a list of candidate SNPs. The Galaxy platform generates the files needed for plotting SNPs with the R package ggplot2 and for identifying candidate SNPs with SnpEff. Ourprotocol will guidethe user step-by-step through the Galaxy platform, chromosome plotting, and SnpEff.