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@unige.ch