20 Jun
2012
20 Jun
'12
4:26 p.m.
Hello all,
We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st at
2pm CET.
On the agenda:
- program for the Barcelona meeting (see attached draft)
- data and analysis updates
- Jonas from Uppsala will present some QC results
- Liliana from EBI will present "Conjoined genes in human populations"
- Mar from EBI will present "Ubiquity vs specificity of gene and isoform
expression across populations" (if there's time)
Call details are:
from outside spain; 0034917911859
from spain; 900800678
Access code; 3160100
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
21 Jun
21 Jun
9:29 a.m.
Hello!
Here are my slides for the TC today. Its many slides but I will be brief
and Olof will present this again at the Barcelona meeting.
/Jonas
On 06/20/2012 04:26 PM, Tuuli Lappalainen wrote:
Hello all,
We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st
at 2pm CET.
On the agenda:
- program for the Barcelona meeting (see attached draft)
- data and analysis updates
- Jonas from Uppsala will present some QC results
- Liliana from EBI will present "Conjoined genes in human populations"
- Mar from EBI will present "Ubiquity vs specificity of gene and
isoform expression across populations" (if there's time)
Call details are:
from outside spain; 0034917911859
from spain; 900800678
Access code; 3160100
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
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
2:06 p.m.
Hi,
did I mix up something with the time or the code? I'm apparently alone
connected to the system, listening to sort of elevator music..
Anybody joins?
Cheers, micha
--
Dr. Michael Sammeth, GL Functional Bioinformatics
Phone: +34-934-020-580, http://www.cnag.eu
Centre Nacional d'Anàlisi Genòmica (CNAG), PCB
Baldiri Reixac 4-6, Room 02A8, 08028 Barcelona
On Wed, Jun 20, 2012 at 4:26 PM, Tuuli Lappalainen <
Tuuli.Lappalainen(a)unige.ch> wrote:
Hello all,
We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st at
2pm CET.
On the agenda:
- program for the Barcelona meeting (see attached draft)
- data and analysis updates
- Jonas from Uppsala will present some QC results
- Liliana from EBI will present "Conjoined genes in human populations"
- Mar from EBI will present "Ubiquity vs specificity of gene and isoform
expression across populations" (if there's time)
Call details are:
from outside spain; 0034917911859
from spain; 900800678
Access code; 3160100
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)22-3795550tuuli.lappalainen(a)unige.ch
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
2:07 p.m.
Hi,
we are also alone. Apparently a "chairperson" needs to connect.
Regards,
Thomas
M.Sammeth wrote:
Hi,
did I mix up something with the time or the code? I'm apparently alone
connected to the system, listening to sort of elevator music..
Anybody joins?
Cheers, micha
--
Dr. Michael Sammeth, GL Functional Bioinformatics
Phone: +34-934-020-580, http://www.cnag.eu
Centre Nacional d'Anàlisi Genòmica (CNAG), PCB
Baldiri Reixac 4-6, Room 02A8, 08028 Barcelona
On Wed, Jun 20, 2012 at 4:26 PM, Tuuli Lappalainen
<Tuuli.Lappalainen(a)unige.ch <mailto:Tuuli.Lappalainen@unige.ch>> wrote:
Hello all,
We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st
at 2pm CET.
On the agenda:
- program for the Barcelona meeting (see attached draft)
- data and analysis updates
- Jonas from Uppsala will present some QC results
- Liliana from EBI will present "Conjoined genes in human populations"
- Mar from EBI will present "Ubiquity vs specificity of gene and
isoform expression across populations" (if there's time)
Call details are:
from outside spain; 0034917911859
from spain; 900800678
Access code; 3160100
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 <tel:%2B41-%280%2922-3795550>
tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch>
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
<mailto:Geuvadis_rna_analysis@lists.crg.es>
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
------------------------------------------------------------------------
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
--
Thomas Wieland
PhD student
Institute of Human Genetics
Tel: +49 89 3187 2169
Fax: +49 89 3187 3297
http://ihg.helmholtz-muenchen.de
*Helmholtz Zentrum München*
Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
Ingolstädter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe
Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum
Registergericht: Amtsgericht München HRB 6466
USt-IdNr: DE 129521671
2:07 p.m.
Also Irina and Peter from Leiden are there, but without the chair person we can't
start I think...
________________________________________
From: geuvadis_rna_analysis-bounces(a)lists.crg.es
[geuvadis_rna_analysis-bounces(a)lists.crg.es] on behalf of M.Sammeth [msammeth(a)pcb.ub.cat]
Sent: Thursday, June 21, 2012 2:06 PM
To: Tuuli Lappalainen
Cc: geuvadis_rna_analysis(a)lists.crg.es
Subject: Re: [Geuvadis_rna_analysis] Analysis group TC June 21st
Hi,
did I mix up something with the time or the code? I'm apparently alone connected to
the system, listening to sort of elevator music..
Anybody joins?
Cheers, micha
--
Dr. Michael Sammeth, GL Functional Bioinformatics
Phone: +34-934-020-580, http://www.cnag.eu
Centre Nacional d'Anàlisi Genòmica (CNAG), PCB
Baldiri Reixac 4-6, Room 02A8, 08028 Barcelona
On Wed, Jun 20, 2012 at 4:26 PM, Tuuli Lappalainen
<Tuuli.Lappalainen@unige.ch<mailto:Tuuli.Lappalainen@unige.ch>> wrote:
Hello all,
We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st at 2pm CET.
On the agenda:
- program for the Barcelona meeting (see attached draft)
- data and analysis updates
- Jonas from Uppsala will present some QC results
- Liliana from EBI will present "Conjoined genes in human populations"
- Mar from EBI will present "Ubiquity vs specificity of gene and isoform expression
across populations" (if there's time)
Call details are:
from outside spain; 0034917911859
from spain; 900800678
Access code; 3160100
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<tel:%2B41-%280%2922-3795550>
tuuli.lappalainen@unige.ch<mailto:tuuli.lappalainen@unige.ch>
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis@lists.crg.es<mailto:Geuvadis_rna_analysis@lists.crg.es>
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
4:02 p.m.
New subject: [Geuvadis_rna_analysis] Analysis group TC June 21st - Minutes
Hello,
Here are the minutes of today's analysis group call. The next call will
be in one week, June 28th at 2pm CET.
- Everything is pretty much set for the Barcelona analysis group
meeting. Tuuli and Gabrielle will put together the final program &
practical info. Most people are staying in H10 Marina - if you haven't
arranged your accommodation yet and want to stay there, contact them
directly: tel (34) 93 309 79 17, fax (34) 93 309 97 62, group booking
code 11596
- Genotype data is now available on the ftp site also for the imputed
samples.
- Splice junction quantifications should be done within days, some
N-TARs in a couple of weeks, other labs are also analyzing data
- Thasso will write documentation about the GEM mapping in the wiki -
some of the parameters about multimapping reads etc. are important to
know for analysts
- Leiden needs insert size distributions; Tuuli uploaded them in
/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/qc/insert_size
- Natalja will create wig files from a couple of samples so that we can
test visualizing them in the Ensembl browser
- Thasso will start running simulated read mappings (single end, no
split mapping needed), after which Tuuli will finish ASE
- Tuuli will do sample swap checks for the imputed samples too, and look
into other QC aspects
- Jonas presented slides about mRNA QC analysis. Some outliers and some
lab effects but no major concerns, replicates show good signals.
- We'll have Liliana's and Mar's presentations next week
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
On 6/20/12 4:26 PM, Tuuli Lappalainen wrote:
Hello all,
We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st
at 2pm CET.
On the agenda:
- program for the Barcelona meeting (see attached draft)
- data and analysis updates
- Jonas from Uppsala will present some QC results
- Liliana from EBI will present "Conjoined genes in human populations"
- Mar from EBI will present "Ubiquity vs specificity of gene and
isoform expression across populations" (if there's time)
Call details are:
from outside spain; 0034917911859
from spain; 900800678
Access code; 3160100
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
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
4502
days inactive
4503
days old
geuvadis_rna_analysis@lists.crg.es
5 comments
5 participants
participants (5)
-
I.Pulyakhina＠lumc.nl -
Jonas Carlsson -
M.Sammeth -
Thomas Wieland -
Tuuli Lappalainen