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I found the same questions on SeqAnswers, though they out of date (year 2010 and 2014).