[Geuvadis_rna_analysis] main paper

Hello, In order to keep things rolling for the main paper, I've put together a list of action items for all of us, as well as an early draft of supplemental figures and tables. The main figure draft has been updated a bit as well. There are plenty of placeholders for us to fill, and let's discuss these on the call tomorrow - these are definitely open for discussion. I'd also like to emphasize that now when we're finalizing the analysis and I'm trying my best to put it all together, we should have subgroup or one-on-one calls if you don't understand what I'm asking from you, or if it seems that I'm misunderstanding your analysis. best, Tuuli The action items are here (as well as in the attached document): Everyone - Text for the supplement: methods, results, and conclusions of your analysis. - Good-quality figures (see doc for details) - Deadline: October 20 Tuuli - finish splicing QTLs - plenty of downstream analysis of QTLs - rare variant mapping - Loss-of-function ASE NMD stats - ASAS / ASE sharing analysis - finish some QC analyses - ...a zillion other things Micha - Coordinate documentation of mRNA mapping and transcript quantification - Coordinate splicing paper - some plot(s) of splicing variation (coefficient of variation? Annotated/novel junctions vs population freq?) - Final figures: - gene discovery plot that works in smaller space - splice score distributions - allele frequency distributions for splicing score categories (DAF from annotations in vcf) Marc - miRNA-mRNA correlation analysis Jean - quantitative analysis of population differences (e.g. GBR-CEU looks visually the same as GBR-YRI, but is this really true numerically? Compare all population pairs) - prettier figures of transcript quantification stats - prettier figures of quantitative vs qualitative variation Mar & Pedro - Prepare a Venn-diagram of splice/expression differentiated genes and plot some examples Liliana - quantitative values of fusion events for QTL analysis - prettier frequency and distance plots Manny - Stop-gained NMD compensation - Splice effect modeling with Micha's scores - NMD prediction - Coordinate LoF paper Peter - coordinate QC paper Irina - results of repeat analysis - quantitative values for QTL analysis? Maarten - miRNA-mRNA correlation analysis Matthias - prettier plots that illustrate soft splicing variation: - phenomenon in general: the lineplot that shows the distances from the major spliceoform - population variation in an analogous way to Jean's analysis Daniela - results of n-TAR analysis - quantitative values of n-TARs for QTL analysis Thomas - results of RNA editing analysis - quantitative values of editing for QTL analysis Monkol & Daniel - annotation statistics (variants in each category) -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch