Considerable time in computational genomics is spent on overlapping different features of the genome. Each feature can be represented with a genomic interval within the chromosomal coordinate system. Overlapping mapped reads from high-throughput sequencing experiments with genomic features such as exons, promoters, and enhancers can also be classified as operations on genomic intervals. However, in these types of experiments and the following analysis, one usually ends up with genomic regions that are bound by transcription factors. Since each mapped read has a start and end position the genome, mapped reads can be thought of as genomic intervals stored in a file. The reads from sequencing machines are usually pre-processed and aligned to the genome with the help of specific bioinformatics tools. The Rsamtools package has functions to query BAM files. The function we will use in the first example is the countBam() function, which takes input of the BAM file and param argument.