What are the major differences between the use cases of a shot-gun genome and an mRNA capture transcriptome? Especially when it comes to downstream analyses such as looking for orthology, and selection analysis.
From what I can visualize in my head, I can come up with the following points:
The genome has the structural data, information on chromosomes, and haplotypes while the transcriptome lacks this information.
The genome records the SNPs more directly than transcriptomes. I might be thinking of this wrong but the genomes would have the actual bases and we can then compare the bases between the genomes but for transcriptomes differences in expression would show up as presence/absence variations that have no way of being traced back?
The transcriptomes should be easier to work with when it comes to computational requirements since they tend to be 25 to 50 times smaller than genomes.
I could be completely wrong about the points I listed and could be missing something major. What do you guys think?