Dear all,
Here are minutes of the Geuvadis analysis
group TC on January 12.
The next call has to be pushed forward by one
week to February
2 at 2pm.
We'll continue with the normal
schedule after that, so the one after that
will be February 9.
best regards,
Tuuli
Action items:
- Tuuli:
Set up a call for next week to discuss
imputation details with Natalja, Micha, Tim.
Continue masked mapping tests
- Esther, Peter, Natalja:
Send an outline of you miRNA analysis
pipeline to the analysis group mailing list
- Everyone:
Think and discuss in your lab about the
analyses that you'd want to do (lead and/or
participate) with this dataset, by the next
call
- Micha:
Continue mapping tests
- Attending:
Tuuli, Micha, Esther, Ivo, Tim, Thomas x2,
Mathias, Peter, Olof, Matthias, Natalja
- Sequencing:
Most of the labs will be able to meet the
initial deadline of Feb 15 despite the delays
in kit delivery, which is great. We agreed to
keep the very last deadline of March 15; all
the samples and reruns should be done and data
submitted by then.
- Genotypes:
We need to impute about 40 samples that are
not in 1000g Phase 1 (they have Omni 2.5M
haplotypes). Natalia/EBI could probably do
this, and Tuuli, Micha and Tim & co. want
to be involved/informed too. This should be
done within a month.
- miRNA
analysis pipeline: The labs who
have experience of miRNA analysis will send
around details of how they map and quantify
miRNAs. We'll discuss on the next call how we
should analyze them.
- A new
collaboration: Mark McMarthy
from
Oxford
is a long-term collaborator of Manolis.
They've developed a new kind of a burden test
to look at rare variant effects, and expressed
interest in doing some analysis with the
Geuvadis data. People were positive about
this, and Mark's postdoc Manuel Rivas will
present their plans in a future TC.
- Analysis
plans: Tuuli would like to
coordinate the future analyses so that the
essentials get done and there's no unnecessary
overlaps. For this we also need to assign
people who will lead/participate/be informed
for each set of analysis. In the next call
we'll start putting together a list of what
will be done and by whom.
- Analysis
group face-to-face meeting: It
would be good to get together to discuss in
real life once the data is ready and gone
through basic pipelines - maybe around April.
- mRNA
mapping: The GEM paper will be
submitted soon, so we might want to use
Micha's pipeline for mapping, quantification
and normalization as the basic approach. Micha
presented some slides about an approach that
they're developing for SNP calling from RNAseq
data, based on excessive mapping. Tuuli
presented results suggesting that reference
allele mapping bias affects exon
quantifications. We should correct for it e.g.
by mapping to a masked reference.
--
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