A common challenge is to find and count reads that have aligned outside of annotated regions. In an RNAseq experiment, these reads can represent non-annotated genes and novel transcripts. Essentially, we have some genes we know about and can see that they are transcribed as they have aligned read coverage, but other transcribed regions do not fall in any annotations and we want to know the locations of the alignments of the reads representing them. In this recipe, we'll look at a deceptively straightforward technique for finding such regions.