Hello, I was reading this paper (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0970-8) when I encountered the following sentence:

Note that in order to estimate the transcript abundances from the transcript-compatibility counts, a read-generation model is needed to resolve the multi-mapped reads

I think I get a rough idea of what a read-generation model means - if you model how reads are generated for each isoform expression profile, you can then estimate isoform expression given a set of reads.

Is my interpretation correct? Could anybody point me to some literature to learn more about this topic? What are common read-generation models? What read-generation models do current tools use?

Thanks a lot!!