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
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