I am working on a virtual project for WGS combined with RNA seq for annotation. The RNA will be sequenced using PacBio Isoseq (Sequel II, HiFi-reads). With some research, I found that StringTie2 is useful for this. In their release paper , they sometimes mention previous alignment or mapping with TopHat or minihat, but I don't find a manual where they say the same. Now I don't know what is supposed to be the input of StringTie2: raw RNA reads, or a mapped BAM-file?