[Geuvadis_rna_analysis] RNAseq paper

Dear all, The Geuvadis RNAseq paper was rejected this morning. We've decided with Manolis that we should make an appeal, and we have already been in touch with Magdalena about this. We'll need to send her a response letter in a couple of days (see the attachment with reviewer's comments and a rough response draft). It ain't over til it's over. Since we were going to have a call soon anyway, let's have a *TC on Thursday the 24th at 4pm CET*. Before that, I'd be happy to hear your *comments to the response letter (deadline: immediately)*. There's a couple of bigger items to discuss, and specific questions to a few of you - see below. There won't be a lot of new analysis to do if we're given the chance to revise. Questions: - Do we drop non-essential analyses as #2 suggests? This would mean RNA editing, maybe fusions and subtle splicing. I'm not keen to, but if people think it would improve the overall quality of the paper... - Should we restructure the supplement by topic instead of methods/figures/tables? Need to ask Magdalena too. - Andrew & Natalja: Can we add a data slicing and download function to the browser (or a separate site linked from the browser)? - Jean & Mar: How is the qualitative/quantitative analysis affected by low-abundance transcripts? Will the results change if the threshold is different? - Jean, Mar, Pedro, Micha (and myself): #2 raises an important question (really!): most of transcript variation is explained by transcript ratio differences, but we find very few QTLs for this. Why do you think this is? Is all that variation really just random/environmental/epigenetic? - Jean: #3 suspects that the 3% of transcriptome variation explained by population could be just random - how do we respond to this? - Manny: What could we do to add novelty value to NMD analysis? - Gabrielle: Is it possible to make a read-only password for the wiki? We could give one to the reviewers just so that they can see it. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine , and Department of Genetic Medicine and Development, University of Geneva Email: tuuli.e.lappalainen(a)gmail.com / tlappala(a)stanford.edu Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA