Now that we have a bam file with only the reads we want included, we can do some more sophisticated analysis using bedtools. Bedtools changes from version to version, and here we are using version 2.22, the newest version, and what is currently installed on stampede.
Exercise 1: convert bam to fastq and look at the quality scores
Exercise 2: Convert bam to bed using bamtobed
Exercise 3: Find the coverage of your bed file over the genome
Exercise 4: Intersect two experiment using intersect
Exercise 5: Use bedtools merge to merge two experiments
