I recently started grad-school and have no background working with sequencing data :( As the first thing to do my supervisor asked me to look at these two files "XXX.bam" and "XXX.bam.bai" and figure out if they are the same files (just one indexed) or they are different. I figured out that since these files have exact same name, but one with additional ".bai" at the end, it looks XXX.bam.bai is the index form of the XXX.bam, but I am not completely sure. Can some one please give me a hint how to make sure if the files are the same or not? What program I can use to generate indexed bam? (SAM?! I just heard about it, never had a chance to work with yet) and by what program I can visualize them?
Thank you so much....