Novel discovery is always a tricky task. If you haven't done already, I'd optimise your process of analysing your known genes / transcripts before you start at looking into novel elements. Cufflinks and StringTie are your major two options, run them on each of your samples, then merge them. Once they're merged, you have a GTF file that shows every potential transcript in all your samples (heads up, it'll likely be a lot). You can then quantify against this GTF file and perform differential expression. Finding lowly expressed novel transcripts from RNA Seq data is an extremely difficult challenge, as the nature of short read sequencing makes it very difficult in the first place! Depending on the depth of your sequencing will decide what you can essentially discover, and quantify. Whatever disease you're studying, and what you're sampling (blood, tissue specific, isolated cells), will also play into the equation of what you can find too. The good news is that you have a pretty decent sample size with 100 samples!