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(a)unige.ch