What are the advantages and disadvantages of mapping to genome or transcriptome? Is there a good quality transcriptome available for Macaca Mulata and human?
The advantage of mapping to transcriptome is definitely the time, it takes more time to map reads to the genome. I also head that for some species a good quality transcriptome is not available so it is preferred to map to genome and the other way round. I could not find any comparison paper where the same reads were mapped to genome and transcriptome.
I found the same questions on SeqAnswers, though they out of date (year 2010 and 2014).
Some additional advantages of using the transcriptome (besides speed):
Depending on the quality of the macaque transcriptome, one option may be de novo assembly of both H. sapiens and M. mulata. Annotate both with the human proteome, and quantify with Salmon as mentioned.