2 Feb
2012
2 Feb
'12
1:08 p.m.
Hello all,
Here are the call details for today's TC:
Spain
902 125 136
Other countries
+34 91 495 18 99
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
-------- Original Message --------
Subject: Geuvadis RNAseq AG call on Thursday
Date: Tue, 31 Jan 2012 18:53:51 +0100
From: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch>
To: geuvadis_rna_analysis(a)lists.crg.es
Hello all,
We'll have out next Geuvadis analysis group TC on Thursday January 2 at
2pm.
Lots of things on the agenda:
- sequencing updates
- analysis group face-to-face meeting: time, duration, location
- abstract for the Biology of Genomes meeting at Cold Spring Harbor
- Marc will present results of the DNA contamination analysis
- miRNA data processing and QC
- analysis plans (see below)
As we discussed on the last call, I'd like to start putting together a
plan of what we all eventually want to do with the data. The data is of
course shared and everyone is free to do what they want, but we need to
make sure that the essentials get done and that there's no unnecessary
overlap. As a starting point for discussion, take a look at the analysis
breakdown draft that I wrote
(https://docs.google.com/document/d/1_LAkv0NGSrXU6LSsyhN_GnZB4WRanl-e993U_0I…),
and feel free to edit it before/during 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
2 Feb
2 Feb
1:22 p.m.
Hi,
here are some slide for the QC result presentation on 24 test samples.
bests,
marc
On 02.02.2012, at 13:08, Tuuli Lappalainen wrote:
Hello all,
Here are the call details for today's TC:
Spain
902 125 136
Other countries
+34 91 495 18 99
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
-------- Original Message --------
Subject: Geuvadis RNAseq AG call on Thursday
Date: Tue, 31 Jan 2012 18:53:51 +0100
From: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch>
To: geuvadis_rna_analysis(a)lists.crg.es
Hello all,
We'll have out next Geuvadis analysis group TC on Thursday January 2 at
2pm.
Lots of things on the agenda:
- sequencing updates
- analysis group face-to-face meeting: time, duration, location
- abstract for the Biology of Genomes meeting at Cold Spring Harbor
- Marc will present results of the DNA contamination analysis
- miRNA data processing and QC
- analysis plans (see below)
As we discussed on the last call, I'd like to start putting together a
plan of what we all eventually want to do with the data. The data is of
course shared and everyone is free to do what they want, but we need to
make sure that the essentials get done and that there's no unnecessary
overlap. As a starting point for discussion, take a look at the analysis
breakdown draft that I wrote
(https://docs.google.com/document/d/1_LAkv0NGSrXU6LSsyhN_GnZB4WRanl-e993U_0I…),
and feel free to edit it before/during 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
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
-------------------------------------------------------------------
Dr. Marc Sultan
Dept. Vertebrate Genomics
Max Planck Institute for Molecular Genetics
Ihnestr. 63-73
14195 Berlin
Germany
Tel.+49308413-1349
Mob. +49 175 585 3465
Fax +49308413-1128
sultan(a)molgen.mpg.de
2:24 p.m.
example of Geneva read identifier
@HWI-ST661:130:C037KACXX:6:1101:1387:2156 1:Y:0:CTTGTA
On Thu, Feb 2, 2012 at 1:22 PM, Marc Sultan <sultan(a)molgen.mpg.de> wrote:
Hi,
here are some slide for the QC result presentation on 24 test samples.
bests,
marc
On 02.02.2012, at 13:08, Tuuli Lappalainen wrote:
Hello all,
Here are the call details for today's TC:
Spain****
902 125 136****
Other countries****
+34 91 495 18 99****
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)22-3795550tuuli.lappalainen(a)unige.ch
-------- Original Message -------- Subject: Geuvadis RNAseq AG call on
Thursday Date: Tue, 31 Jan 2012 18:53:51 +0100 From: Tuuli Lappalainen
<Tuuli.Lappalainen(a)unige.ch> <Tuuli.Lappalainen(a)unige.ch> To:
geuvadis_rna_analysis(a)lists.crg.es
Hello all,
We'll have out next Geuvadis analysis group TC on Thursday January 2 at
2pm.
Lots of things on the agenda:
- sequencing updates
- analysis group face-to-face meeting: time, duration, location
- abstract for the Biology of Genomes meeting at Cold Spring Harbor
- Marc will present results of the DNA contamination analysis
- miRNA data processing and QC
- analysis plans (see below)
As we discussed on the last call, I'd like to start putting together a
plan of what we all eventually want to do with the data. The data is of
course shared and everyone is free to do what they want, but we need to
make sure that the essentials get done and that there's no unnecessary
overlap. As a starting point for discussion, take a look at the analysis
breakdown draft that I wrote
(https://docs.google.com/document/d/1_LAkv0NGSrXU6LSsyhN_GnZB4WRanl-e993U_0I…),
and feel free to edit it before/during 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)22-3795550tuuli.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
-------------------------------------------------------------------
Dr. Marc Sultan
Dept. Vertebrate Genomics
Max Planck Institute for Molecular Genetics
Ihnestr. 63-73
14195 Berlin
Germany
Tel.+49308413-1349
Mob. +49 175 585 3465
Fax +49308413-1128
sultan(a)molgen.mpg.de
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
--
Dr. Michael Sammeth, 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
4:26 p.m.
New subject: [Geuvadis_rna_analysis] Geuvadis RNAseq AG call - minutes
Hello,
Here are the minutes of the Geuvadis RNAseq analysis group TC. *The next
call will be on February 9 at 2pm*.
- Sequencing is going well, and we're on schedule to keep the final
deadline of March 15 for fastq uploads.
- Tuuli will resend the instructions for data processing, file naming
and ftp upload. These (as all other guidelines) can always be found from
the wiki.
- We'll have a face-to-face meeting for the analysis group in mid-April.
Please fill in the Doodle for the dates before the next
call:http://www.doodle.com/24a4i3n8bkynhpwx . Geneva, Berlin and Leiden
are volunteering to host, let's decide that next week.
- We'll submit an abstract for the Biology of Genomes meeting at Cold
Spring Harbor in mid-May. Tuuli will circulate the abstract draft later.
- Marc from Berlin presented some slides of QC analysis of mRNAseq data,
the main point being that the quality looks good and DNA contamination
is not an issue.
- miRNA QC steps were discussed. Many of the labs don't have the
experience and pipelines to do initial QC for the data that they
produce. Tuuli will upload Geneva's miRNA fastq files to the ftp site so
that people with more experience can take a look and define some basic
QC criteria asap (I'm sorry but I forgot who promised to do this, can
you send me an email?).
- The draft of analysis plans was discussed. It's been added to the wiki
(analysis page), feel free to edit it further anytime.
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 2/2/12 1:08 PM, Tuuli Lappalainen wrote:
Hello all,
Here are the call details for today's TC:
Spain
902 125 136
Other countries
+34 91 495 18 99
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
-------- Original Message --------
Subject: Geuvadis RNAseq AG call on Thursday
Date: Tue, 31 Jan 2012 18:53:51 +0100
From: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch>
To: geuvadis_rna_analysis(a)lists.crg.es
Hello all,
We'll have out next Geuvadis analysis group TC on Thursday January 2 at
2pm.
Lots of things on the agenda:
- sequencing updates
- analysis group face-to-face meeting: time, duration, location
- abstract for the Biology of Genomes meeting at Cold Spring Harbor
- Marc will present results of the DNA contamination analysis
- miRNA data processing and QC
- analysis plans (see below)
As we discussed on the last call, I'd like to start putting together a
plan of what we all eventually want to do with the data. The data is of
course shared and everyone is free to do what they want, but we need to
make sure that the essentials get done and that there's no unnecessary
overlap. As a starting point for discussion, take a look at the analysis
breakdown draft that I wrote
(https://docs.google.com/document/d/1_LAkv0NGSrXU6LSsyhN_GnZB4WRanl-e993U_0I…),
and feel free to edit it before/during 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
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
4642
days inactive
4642
days old
geuvadis_rna_analysis@lists.crg.es
3 comments
3 participants
participants (3)
-
M.Sammeth -
Marc Sultan -
Tuuli Lappalainen