Hello all,
Greetings from Cold Spring Harbor! The Geuvadis RNAseq poster was really
popular and lots of people were impressed by the dataset and the
analyses that we put together for the poster. There is definitely a lot
of interest in the paper and the dataset.
Now that there are so many people waiting for the paper and the data to
come out, let's keep on working to make sure we'll get it done sooner
rather than later. A couple of questions/issues:
- FYI to everyone, the GEM manuscript is still not submitted despite
many promises to get it done by the end of April.
- Micha/Thasso, what's the situation regarding the gem-bam conversions?
Are you running them and if not, can you start asap? We need to make
sure that if the manuscript gets submitted and we can decide to use GEM
(I wish that this was a question of when and not if), there's no delay
from this.
- genotype data of the Phase2 samples: I talked with Bryan Howie
(developer of IMPUTE2), and he said that including rare variants and
indels in the reference panel should be fine. Natalja/Thomas, am I
correct that we already had chr1 results where imputation was done with
the full Phase2 set + the total Phase1 without any additional variant
filters, and this looked pretty good? On another note, I learned that
the Phase2 genotype calls are almost there - I'm discussing with people
from the Broad if we could use them and if that would give us better
data than imputing.
cheers,
Tuuli
--
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
Hi all,
We'll have a Geuvadis RNAseq analysis group TC on Thursday May 3rd at 2pm.
On the agenda:
- Tuuli will present the Biology of Genomes poster
- Other analysis updates
- Steps needed to get a final freeze for analysis by the end of May
- Analysis group meeting in Barcelona
- Mailing lists
Call details:
Spain 902 125 136
Other countries +34 91 495 18 99 <tel:%2B34%2091%20495%2018%2099>
Participants' Pin-code: 764989*
best regards,
Tuuli
--
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
Dear all,
We will have the next Geuvadis analysis group meeting in Barcelona in
July 9-10. More info will follow around the end of May.
best regards,
Tuuli
--
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
Hi all,
Here's the latest version of the poster to discuss on the call.
best regards,
Tuuli
--
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
Dear All, thank you very much for filling in the doodle.
We'll have the next TC on Thursday 26th April at 11am
Date and time
Thursday 26th April at 11am
Ready-Access Number:
900800678
Secondary Ready-Access Number:
+34 917911859
7-Digit Access Code:
3160100
Tentative agenda:
- status of the data
- updates from the analysis group meeting
- analysis plans
- Biology of Genomes poster draft
- future meetings
The next Analysis meeting will take place in Barcelona and anyone interested is welcome to join,
here is the doodle for the next meeting: http://www.doodle.com/z7a3mq92b9syz9xg
Conference code:
Best,
Tuuli and Gabrielle
Gabrielle Bertier
Scientific Project Manager
International Collaboration Office
CRG, Center for Genomic Regulation
Carrer Dr. Aiguader, 88
08003 Barcelona, España
Tel: +34933160374
Mobile: +34639960656
email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es>
web: www.geuvadis.eu
From: geuvadis_wpl-bounces(a)lists.crg.es [mailto:geuvadis_wpl-bounces@lists.crg.es] On Behalf Of Tuuli Lappalainen
Sent: 17 April, 2012 5:22 PM
Cc: geuvadis_rnaseq(a)lists.crg.es; geuvadis_wpl(a)lists.crg.es
Subject: Re: [Geuvadis_wpl] GEUVADIS RNAseq General Update
Dear all,
Please fill in the Doodle for a TC with the whole Geuvadis RNAseq group by Wednesday noon.
best regards,
Tuuli
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<mailto:tuuli.lappalainen@unige.ch>
On 4/12/12 11:10 AM, Gabrielle Anne Bertier wrote:
Dear all,
At the request of Tuuli, please fill in the doodle<http://doodle.com/3i5f4wt28ez596sx> to schedule a TC with the whole RNAseq group for an update on the data analysis.
Tentative agenda:
- status of the data
- updates from the analysis group meeting
- analysis plans
- Biology of Genomes poster draft
- future meetings
Kind regards,
Gabrielle
doodle full link: http://doodle.com/3i5f4wt28ez596sx
Gabrielle Bertier
Scientific Project Manager
International Collaboration Office
CRG, Center for Genomic Regulation
Carrer Dr. Aiguader, 88
08003 Barcelona, España
Tel: +34933160374
Mobile: +34639960656
email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es>
web: www.geuvadis.eu
_______________________________________________
Geuvadis_wpl mailing list
Geuvadis_wpl(a)lists.crg.es<mailto:Geuvadis_wpl@lists.crg.es>
http://davinci.crg.es/mailman/listinfo/geuvadis_wpl
Dear all,
Enclosed please find a draft of the Geuvadis RNAseq poster that I'll be
presenting next week at the Biology of Genomes meeting in Cold Spring
Harbor. Small changes are still possible until Thursday, so comments are
welcome.
I think we managed to put together some pretty cool results in a very
short time - my special thanks go to Micha, Marc F, Jean and Manny for
contributing results and figures for the poster.
best regards,
Tuuli
--
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
Dear all,
The next Geuvadis analysis group meeting will take place in Barcelona in
late June or early July. If you'd be interested in attending, please
fill the Doodle to find the best time for the 2-day meeting:
http://www.doodle.com/z7a3mq92b9syz9xg
best regards,
Tuuli
--
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
Hello all,
Apologies for the extremely late notice, but there's a skype call on
Wednesday morning at 9am CET to discuss quality control analyses (with
at least myself, Olof, Jonas and Marc F attending). Feel free to join if
you like, and get this message on time. I completely forgot to tell
about this before, sorry about that.
We'll have the normal analysis group TC on Thursday at 2pm, I'll send a
separate email about that.
best regards,
Tuuli
--
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