Dear all
As I said I will not be able to attend the calls at this day and time.
Jean Monlong from my group will bea ttending. He actually attended today
as well
Roderic
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
--
(1) Centre de Regulacio Genomica
(2) Universitat Pompeu Fabra
Dr. Aiguader, 88 +34 93 3160110 ph
E-08003 Barcelona +34 93 3969983 fax
email: roderic.guigo(a)crg.cat
http://big.crg.cat
RECOMB 2012 in Barcelona,
http://recomb2012.crg.cat/
10 PhD fellowships,
http://www.crg.eu/lacaixa_fellowships
3 fellowships for interdisciplinary post-doctoral studies
http://www.crg.es/interpod