This protocol describes mapping short sequence reads to a reference genome using several programs. The example in this protocol starts with a ChIP-seq data set in FASTQ format, aligns the reads to the human genome using Bowtie, and uses some useful utilities of SAMtools and BEDTools. SAMtools and BEDTools are two collections of executables for manipulating the results of short-read aligners. By combining these tools, one can summarize and visualize alignments produced by Bowtie and perform basic analysis, such as determining the number of reads that are mapped to a certain gene. These tools can also be easily incorporated into computational pipelines of more complex analyses.