I inherited an RNA-Seq project with the goal of looking at differential expression across different environmental conditions and species in protists (using SOLiD, although probably the question is more general), that originally used transcripts as the mapping target rather than the genomes, largely for technical rather than scientific reasons. When I inherited it, I moved to mapping to the genomes, but the results don't correlate as much as one would think to the previous results (based on the same reads) and the experimental collaborator likes the transcript based results better as they behave closer to what he expects. So, one possibility is to ignore the genomes and go back to the transcripts for mapping.
What I am asking is if there is any literature dealing with the difference between transcriptome and genome mapping for RNA-seq and are there any scientific reasons to support transcriptome mapping even if the genome is available? I have tried to do a literature search myself, but I haven't seen anything that addresses the issue. Does anyone have any insight on this issue?
Thanks,
Jonathan
What I am asking is if there is any literature dealing with the difference between transcriptome and genome mapping for RNA-seq and are there any scientific reasons to support transcriptome mapping even if the genome is available? I have tried to do a literature search myself, but I haven't seen anything that addresses the issue. Does anyone have any insight on this issue?
Thanks,
Jonathan
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