19 Jul
2012
19 Jul
'12
10 a.m.
Hello all,
I have drafted an outline for the Geuvadis RNAseq main paper based on
the presentations and discussions at the Barcelona meeting. Please take
a look and let me know if I've forgotten or misunderstood something, or
if you have other suggestions. I will send it to the whole RNAseq group
Friday afternoon, so I'd appreciate if you could send your comments
before 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
19 Jul
19 Jul
5:10 p.m.
Dear Tuuli and others
Thanks for this draft. It looks good. Indeed, focusing the main message paper on the
functional annotation of variants seems good to me. Perhaps that could also be reflected
in the title: Systematic functional annotation of genomic variants by combined DNA and RNA
sequencing
Regarding the qc paper: to exactly trace the sources of batch effects and variation is
rather complicated (we will definitely find GC but other than that, I am not even sure we
will find an effect of RIN values). I believe the main message is that you can do
distributed sequencing, what are best practices, what qc parameters should be quantified,
and how one deals with sources of variability
Ideas from others are more than welcome
Peter
-----Original Message-----
From: geuvadis_rna_analysis-bounces(a)lists.crg.es
[mailto:geuvadis_rna_analysis-bounces@lists.crg.es] On Behalf Of Tuuli
Lappalainen
Sent: Thursday, July 19, 2012 10:01 AM
To: geuvadis_rna_analysis(a)lists.crg.es
Subject: [Geuvadis_rna_analysis] RNAseq paper outline
Hello all,
I have drafted an outline for the Geuvadis RNAseq main paper based on
the presentations and discussions at the Barcelona meeting. Please take
a look and let me know if I've forgotten or misunderstood something, or
if you have other suggestions. I will send it to the whole RNAseq group
Friday afternoon, so I'd appreciate if you could send your comments
before 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
5:57 p.m.
Hi Peter and others,
I agree that finding sources of batch effects would be difficult - I
think I was mostly referring to measuring what data-derived metrics tend
to differ between labs, different runs between labs, etc.
In my preliminary analyses I've already seen that some metrics seem to
have little variation explained by the lab, whereas e.g. insert size and
standard deviation of GC content (but not really GC mean - I don't know
why) are clearly lab-specific. This is actually rather about
consequences than causes of batch effects, but I think looking into this
a little bit would be interesting.
And based on those early analyses, I don't think we're going to have a
problem of not finding significant covariates...there are many, and we
need to be careful not to overcorrect the data.
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 7/19/12 5:10 PM, P.A.C._t_Hoen(a)lumc.nl wrote:
Dear Tuuli and others
Thanks for this draft. It looks good. Indeed, focusing the main message paper on the
functional annotation of variants seems good to me. Perhaps that could also be reflected
in the title: Systematic functional annotation of genomic variants by combined DNA and RNA
sequencing
Regarding the qc paper: to exactly trace the sources of batch effects and variation is
rather complicated (we will definitely find GC but other than that, I am not even sure we
will find an effect of RIN values). I believe the main message is that you can do
distributed sequencing, what are best practices, what qc parameters should be quantified,
and how one deals with sources of variability
Ideas from others are more than welcome
Peter
> -----Original Message-----
> From: geuvadis_rna_analysis-bounces(a)lists.crg.es
> [mailto:geuvadis_rna_analysis-bounces@lists.crg.es] On Behalf Of Tuuli
> Lappalainen
> Sent: Thursday, July 19, 2012 10:01 AM
> To: geuvadis_rna_analysis(a)lists.crg.es
> Subject: [Geuvadis_rna_analysis] RNAseq paper outline
>
> Hello all,
>
> I have drafted an outline for the Geuvadis RNAseq main paper based on
> the presentations and discussions at the Barcelona meeting. Please take
> a look and let me know if I've forgotten or misunderstood something, or
> if you have other suggestions. I will send it to the whole RNAseq group
> Friday afternoon, so I'd appreciate if you could send your comments
> before 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
5004
days inactive
5004
days old
geuvadis_rna_analysis@lists.crg.es
2 comments
2 participants
participants (2)
-
P.A.C._t_Hoen＠lumc.nl -
Tuuli Lappalainen