Would anyone out there like to share their opinions about the relative merits and pitfalls of using the human transcriptome vs. the human genome as a reference for mapping some Solid RNA-Seq runs? I am guessing that this probably comes down to questions about the relative quality of the transcriptome sequence vs. the genome sequence (in other words, how complete is the transcriptome build relative to the genome build) and the relative role of splice-prediction algorithms (e.g. tophat) and their effects on read mapping. Any thoughts out there? To be honest, I don't know a whole lot on how "complete" the human transcriptome is supposed to be (# of tissues, life stages, etc.). I'm just looking for what would be the "best" way to do this. I could run both, but thought I'd start with first principles and go from there as these bam files are huge and a pain to store.
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