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@unige.ch