There are many ways to quantitate transcripts. Some work off aligned BAMs (e.g. RSEM), other pseudoalignment methods can go directly from FASTQs (e.g. Salmon). Salmon is very easy to use, very fast, and highly accurate (and can also work on aligned BAMs if you want to go that route). You'd likely be well-served by reading the salmon papers/docs. The DESeq2 vignette is also a classic "must read" for typical differential gene analysis. There's also a Bioconductor workflow built on the DRIMSeq and DEXSeq packages that walks through a differential transcript usage (DTU) analysis if you've got a need for that.