I have a question about pseudo aligners. I’m using Kallisto and I was wondering if it would count novel rearrangements of known transcripts. For example, suppose I have the following gene consisting of three exons.
If I include this in the kallisto transcriptome and index it I understand that Kallisto will detect and count the intended transcript such as this…
My question is.... What if there were a transcript like this in which the second exon was missing….
Would Kallisto detect and include this in the gene counts?
What about if exon 2 and 3 were swapped, like this…