IGV is a neat graphical software application that takes the sort of files (BAM, BED, bigWig, etc.) you typically get from your friendly neighborhood sequencer and allows you to browse them on your desktop. With BAM files (binary files of alignments), it’s especially handy because you can see each read and where it was placed. If you ordered paired-end sequencing, you can bundle reads by their mate pairs. In this week’s demo, Alejandro is going to show us a special case where looking at alignments is absolutely essential: circular RNA. Download the slides here. We’re giving you some real data from his research, limited to chr1 in order to save space, but if you’ve brought your own, feel free to use it instead!
Before you get started, please make sure to download IGV here. The Broad Institute requires that you register first, but it’s pretty simple and free. I’ve been with them for years and haven’t been hacked yet.