[Geuvadis_rna_analysis] important: action items for the main paper

Hello, I've drafted the main paper and I'll send it to you for comments in 1-2 days. Before that, I want to fill in as many of the missing pieces as possible - I'm working hard on many of these, and some I need from you. We're not far from finish, but not quite there yet either. I've put together a list of action items, some of these I've already discussed with you individually. Please complete as many of these as you can *by Wednesday**6pm*, so that I can have them in the draft before I circulate it. The very serious deadline is on *Saturday* - I'll really need to have these by then if not by Wednesday. cheers, Tuuli - Jean: send sQTL data to Tuuli run Astalavista for GRB sQTLs, and send the numbers for Tuuli for final plotting send Supplementary Fig of transcript quantifications and a legend for it - Micha: finish the analysis of population frequency and annotated/novel junctions splice score distributions (REF & ALT for donor & acceptor): send the values to Tuuli for final plotting. - Gabrielle: figure out what will be the stable www address of the wiki - Matthias calculate how many splice junctions (out of total) have soft splicing in 1) any individual 2) all individuals. - Monkol send supplementary methods text of annotations send a table of variant counts in annotation classes - Natalja: send supplementary methods text of imputation protocol send supplementary methods text of visualization prepare an example plot of the quantification tracks - Peter/Maarten: prepare a prettier network figure (2d) and a legend for that prepare supplementary table of miRNA-mRNA associations send the formulae for supplementary methods - Peter/Irina: I'll get the repeat eQTLs to you on Wednesday morning (sorry for the delay, cluster problems) - after that, analyze them - Jonas: plot read count distributions for miRNA (and replot mRNA if it's easier to make the plots pretty and similar that way) plot gene count histograms for mRNA and miRNA - Manny: get numbers of LoF variants (total and covered by RNAseq data) estimate the number of stop+ that are truly NMD - Tuuli (FYI) analyze causal variant discovery and GWAS causal variants run independent eQTL analysis run sQTL-eQTL overlap run and plot annotation enrichments of sQTLs analyze rare variant mapping if there's time plot MDS for peer-corrected mRNA data polish text, legends and a few figure integrate comments, text and plots from others add references -- 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