[Geuvadis_rna_analysis] main paper draft

Hello all, Here is the draft of the Geuvadis main paper for the analysis group to read and comment. It's still a bit rough, but you get the idea. I'd like to ask you to send comments to me by *Saturday noon* - track changes in word, or write comments in an email. There are still some analysis items and material missing; see the updated action items below and please *complete your tasks**as soon as possible, by Saturday noon at the very latest. * The schedule is tight because we can't let our competitors get too far ahead of us. I'll aim to finish at least 99% of the numbers, results, and changes suggested by you by early next week, after which we circulate the paper with the whole group and submit in early December. There are 5 files: - main paper text (note that links to figures are not necessarily all up to date) - main figures and a table - supplementary methods (feel free to add text here) - supplementary figures (tables are not done yet) - legends for supplementary figures and tables (feel free to add text here) We're not there yet, but I can almost see the light at the end of the tunnel... best, Tuuli - Jean: look a bit into classification of sQTL changes - Gabrielle: figure out what will be the stable www address of the wiki - Matthias update splice junction calculations calculate how many splice junctions (out of total) have soft splicing in 1) any individual 2) all individuals. - Micha: Once/if we have the splice junction updates, analyze population frequency / annotation status distribution - Natalja: send supplementary methods text of imputation protocol send supplementary methods text of visualization continue working on visualization tracks - Peter/Irina: analyze repeat eQTL data - Thomas look at editQTLs - Jonas: replot read and gene count histograms - Manny: get numbers of LoF variants (total and covered by RNAseq data) estimate the number of stop+ that are truly NMD - Tuuli (FYI...a lot of work for me...) analyze causal variant discovery and GWAS causal variants run independent eQTL analysis run and plot annotation enrichments of sQTLs plot MDS for peer-corrected mRNA data polish text, legends and a few figures, integrate comments, text and plots from others, add references analyze rare variant mapping if any time remains (unlikely) -- 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