3 Nov
2011
3 Nov
'11
7:25 p.m.
Dear all,
Enclosed are the Minutes of this afternoon's TC. Action items copypasted
below.
best regards,
Tuuli
*Action items*
-*Tuuli* will take care of the RNA sample shipments (7/14 November) and
inform the contact persons from each lab when the samples are shipped
-*Esther* from Barcelona will email Tuuli further specifications of the
miRNAseq protocol, including the minimum coverage per sample and how
exactly that is defined
-*Tuuli* will send the final version of the sequencing guidelines to all
the labs by November 10
-*Gabrielle* will set up a mailing list for the analysis group
-After the labs have received the samples, there is one major action
item for *all partners*: sequencing!
--
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
8 Nov
8 Nov
8 a.m.
Dear Tuuli
Our sequence facility only sequences 2x100 and not 2x75. Is it allowed to sequence 100bp
and throw away the last 25 nucleotides?
Best
Peter
________________________________
From: geuvadis_rnaseq-bounces(a)lists.crg.es [mailto:geuvadis_rnaseq-bounces@lists.crg.es]
On Behalf Of Tuuli Lappalainen
Sent: Thursday, November 03, 2011 7:26 PM
To: geuvadis_rnaseq(a)lists.crg.es
Subject: [Geuvadis_rnaseq] Geuvadis RNAseq Minutes
Dear all,
Enclosed are the Minutes of this afternoon's TC. Action items copypasted below.
best regards,
Tuuli
Action items
- Tuuli will take care of the RNA sample shipments (7/14 November) and inform the
contact persons from each lab when the samples are shipped
- Esther from Barcelona will email Tuuli further specifications of the miRNAseq
protocol, including the minimum coverage per sample and how exactly that is defined
- Tuuli will send the final version of the sequencing guidelines to all the labs by
November 10
- Gabrielle will set up a mailing list for the analysis group
- After the labs have received the samples, there is one major action item for all
partners: sequencing!
--
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@unige.ch<mailto:tuuli.lappalainen@unige.ch>
8:06 a.m.
That's odd!
In my view there is no problem and I don't see a difference
Cheers,
Manolis
------------------------------------------
Emmanouil (Manolis) Dermitzakis, PhD
Louis-Jeantet Professor
Department of Genetic Medicine and Development
University of Geneva Medical School
1 Rue Michel-Servet (CMU office 9088)
Geneva 1211
Switzerland
Email: emmanouil.dermitzakis(a)unige.ch
Tel: +41 (0) 22 379 5483
Fax: +41 (0) 22 379 5706
website: http://funpopgen.unige.ch/
Admin assistant: Ancilla Stefani,
Tel: +41 22 379 5551
e-mail: Ancilla.Stefani(a)unige.ch
------------------------------------------
P.A.C._t_Hoen(a)lumc.nl wrote:
Dear Tuuli
Our sequence facility only sequences 2x100 and not 2x75. Is it allowed
to sequence 100bp and throw away the last 25 nucleotides?
Best
Peter
------------------------------------------------------------------------
*From:* geuvadis_rnaseq-bounces(a)lists.crg.es
[mailto:geuvadis_rnaseq-bounces@lists.crg.es] *On Behalf Of *Tuuli
Lappalainen
*Sent:* Thursday, November 03, 2011 7:26 PM
*To:* geuvadis_rnaseq(a)lists.crg.es
*Subject:* [Geuvadis_rnaseq] Geuvadis RNAseq Minutes
Dear all,
Enclosed are the Minutes of this afternoon's TC. Action items
copypasted below.
best regards,
Tuuli
*Action items*
- *Tuuli* will take care of the RNA sample shipments (7/14
November) and inform the contact persons from each lab when the
samples are shipped
- *Esther* from Barcelona will email Tuuli further specifications
of the miRNAseq protocol, including the minimum coverage per sample
and how exactly that is defined
- *Tuuli* will send the final version of the sequencing guidelines
to all the labs by November 10
- *Gabrielle* will set up a mailing list for the analysis group
- After the labs have received the samples, there is one major
action item for *all partners*: sequencing!
--
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>
------------------------------------------------------------------------
_______________________________________________
Geuvadis_rnaseq mailing list
Geuvadis_rnaseq(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rnaseq
9:30 a.m.
Hello,
Actually we kind have of the same problem. This is mainly due to the sequencing kits sizes
from Illumina. They are provided either as 50 cycles or 200 cycles kits. Sequencing at 75
bp means breaking up the kit in an inconvenient way. I would therefore also favor to
sequence either 2x50 bp or 2x100, whereby 2x50 bp has been proven to be sufficient for
most of the RNA anaylsis. What's your opinion on this?
Bests,
Marc
On 08.11.2011, at 08:06, Manolis Dermitzakis wrote:
That's odd!
In my view there is no problem and I don't see a difference
Cheers,
Manolis
------------------------------------------
Emmanouil (Manolis) Dermitzakis, PhD
Louis-Jeantet Professor
Department of Genetic Medicine and Development
University of Geneva Medical School
1 Rue Michel-Servet (CMU office 9088)
Geneva 1211
Switzerland
Email: emmanouil.dermitzakis(a)unige.ch
Tel: +41 (0) 22 379 5483
Fax: +41 (0) 22 379 5706
website: http://funpopgen.unige.ch/
Admin assistant: Ancilla Stefani,
Tel: +41 22 379 5551
e-mail: Ancilla.Stefani(a)unige.ch
------------------------------------------
P.A.C._t_Hoen(a)lumc.nl wrote:
-------------------------------------------------------------------
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
Dear Tuuli
Our sequence facility only sequences 2x100 and not 2x75. Is it allowed
to sequence 100bp and throw away the last 25 nucleotides?
Best
Peter
------------------------------------------------------------------------
*From:* geuvadis_rnaseq-bounces(a)lists.crg.es
[mailto:geuvadis_rnaseq-bounces@lists.crg.es] *On Behalf Of *Tuuli
Lappalainen
*Sent:* Thursday, November 03, 2011 7:26 PM
*To:* geuvadis_rnaseq(a)lists.crg.es
*Subject:* [Geuvadis_rnaseq] Geuvadis RNAseq Minutes
Dear all,
Enclosed are the Minutes of this afternoon's TC. Action items
copypasted below.
best regards,
Tuuli
*Action items*
- *Tuuli* will take care of the RNA sample shipments (7/14
November) and inform the contact persons from each lab when the
samples are shipped
- *Esther* from Barcelona will email Tuuli further specifications
of the miRNAseq protocol, including the minimum coverage per sample
and how exactly that is defined
- *Tuuli* will send the final version of the sequencing guidelines
to all the labs by November 10
- *Gabrielle* will set up a mailing list for the analysis group
- After the labs have received the samples, there is one major
action item for *all partners*: sequencing!
--
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>
------------------------------------------------------------------------
_______________________________________________
Geuvadis_rnaseq mailing list
Geuvadis_rnaseq(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rnaseq
_______________________________________________
Geuvadis_rnaseq mailing list
Geuvadis_rnaseq(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rnaseq
10:03 a.m.
Marc
This discussion went on for a while back a few months ago and we have
decided on 2x75
I think we need to stick to that and avoid any further confusion.
If people have to do 2x100 and trim that's fine.
SO we stick to 2x75 but people can do 2x100 and trim BEFORE they map to
assess amount of reads that map and submit data to EBI
Cheers,
Manolis
------------------------------------------
Emmanouil (Manolis) Dermitzakis, PhD
Louis-Jeantet Professor
Department of Genetic Medicine and Development
University of Geneva Medical School
1 Rue Michel-Servet (CMU office 9088)
Geneva 1211
Switzerland
Email: emmanouil.dermitzakis(a)unige.ch
Tel: +41 (0) 22 379 5483
Fax: +41 (0) 22 379 5706
website: http://funpopgen.unige.ch/
Admin assistant: Ancilla Stefani,
Tel: +41 22 379 5551
e-mail: Ancilla.Stefani(a)unige.ch
------------------------------------------
Marc Sultan wrote:
Hello,
Actually we kind have of the same problem. This is mainly due to the
sequencing kits sizes from Illumina. They are provided either as 50
cycles or 200 cycles kits. Sequencing at 75 bp means breaking up the
kit in an inconvenient way. I would therefore also favor to sequence
either 2x50 bp or 2x100, whereby 2x50 bp has been proven to be
sufficient for most of the RNA anaylsis. What's your opinion on this?
Bests,
Marc
On 08.11.2011, at 08:06, Manolis Dermitzakis wrote:
That's odd!
In my view there is no problem and I don't see a difference
Cheers,
Manolis
------------------------------------------
Emmanouil (Manolis) Dermitzakis, PhD
Louis-Jeantet Professor
Department of Genetic Medicine and Development
University of Geneva Medical School
1 Rue Michel-Servet (CMU office 9088)
Geneva 1211
Switzerland
Email: emmanouil.dermitzakis(a)unige.ch
<mailto:emmanouil.dermitzakis@unige.ch>
Tel: +41 (0) 22 379 5483
Fax: +41 (0) 22 379 5706
website: http://funpopgen.unige.ch/
Admin assistant: Ancilla Stefani,
Tel: +41 22 379 5551
e-mail: Ancilla.Stefani(a)unige.ch <mailto:Ancilla.Stefani@unige.ch>
------------------------------------------
P.A.C._t_Hoen(a)lumc.nl <mailto:P.A.C._t_Hoen@lumc.nl> wrote:
-------------------------------------------------------------------
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 <mailto:sultan@molgen.mpg.de>
Dear Tuuli
Our sequence facility only sequences 2x100 and not 2x75. Is it allowed
to sequence 100bp and throw away the last 25 nucleotides?
Best
Peter
------------------------------------------------------------------------
*From:* geuvadis_rnaseq-bounces(a)lists.crg.es
<mailto:geuvadis_rnaseq-bounces@lists.crg.es>
[mailto:geuvadis_rnaseq-bounces@lists.crg.es] *On Behalf Of *Tuuli
Lappalainen
*Sent:* Thursday, November 03, 2011 7:26 PM
*To:* geuvadis_rnaseq(a)lists.crg.es <mailto:geuvadis_rnaseq@lists.crg.es>
*Subject:* [Geuvadis_rnaseq] Geuvadis RNAseq Minutes
Dear all,
Enclosed are the Minutes of this afternoon's TC. Action items
copypasted below.
best regards,
Tuuli
*Action items*
- *Tuuli* will take care of the RNA sample shipments (7/14
November) and inform the contact persons from each lab when the
samples are shipped
- *Esther* from Barcelona will email Tuuli further specifications
of the miRNAseq protocol, including the minimum coverage per sample
and how exactly that is defined
- *Tuuli* will send the final version of the sequencing guidelines
to all the labs by November 10
- *Gabrielle* will set up a mailing list for the analysis group
- After the labs have received the samples, there is one major
action item for *all partners*: sequencing!
--
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>
<mailto:tuuli.lappalainen@unige.ch>
------------------------------------------------------------------------
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Geuvadis_rnaseq mailing list
Geuvadis_rnaseq(a)lists.crg.es <mailto:Geuvadis_rnaseq@lists.crg.es>
http://davinci.crg.es/mailman/listinfo/geuvadis_rnaseq
_______________________________________________
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4699
days inactive
4704
days old
4 comments
4 participants
participants (4)
-
Manolis Dermitzakis -
Marc Sultan -
P.A.C._t_Hoen＠lumc.nl -
Tuuli Lappalainen