In this chapter we assume that we have a collection of reads from all the different (copies of the) transcripts of a gene. We start by showing how to extend read alignment techniques to short RNA reads, and later we show how to exploit the output of genome analysis techniques to obtain an aligner for long reads of RNA transcripts. Our final goal is to assemble the reads into the different RNA transcripts and to estimate the expression level of each transcript. The main difficulty of this problem, which we call multi-assembly, arises from the fact that the transcripts share identical substrings. We illustrate different scenarios, and corresponding multi-assembly formulations, which we then solve using network flow techniques.