How gene-level RPKM is calculated (Brainspan)

[jeremyinseattle]

Hi @JacquelineHeighway. Sorry for the delayed response. I would encourage you to visit the Documentation link on the main BrainSpan website for “Developmental Transcriptome,” as all the information you requested should be included there. I say that I would encourage that because it sounds like you already did and that is where you question comes from. I would suggest contacting the Sestan lab at Yale if you still have questions after reviewing the documentation, as they (along with several other collaborators listed on the main BrainSpan website) were collaborators on this project and were the ones that generated these data files. What I can say is that in most normalization methods, reads are scaled when they cross exon boundaries such that if half the read is in each exon, each exon will get half a read for the RPKM calculation rather than a full read. Such a scaling avoids the issue you bring up.