As Nathan showed you yesterday, the main type of output from aligning reads to a databases is a binary alignment file, or BAM file. These files are compressed, so they can't be viewed using standard unix file viewers such as more, less and head. Samtools allows you to manipulate the bam files - they can be converted into a non-binary format (SAM) and can also be ordered and sorted based on the quality of the alignment. This is a good way to remove low quality reads, or make a bam file restricted to a single chromosome.
Exercise 1: counting mapped vs unmapped reads in a bam file
Exercise 2: counting the number of reads on a chromosome
Exercise 3: Making a sorted bam file with reads that map to multiple places removed
