12 Jan
2012
12 Jan
'12
4:30 p.m.
Dear all,
Here are minutes of the Geuvadis analysis group TC on January 12.
The next call has to be pushed forward by one week to *February 2 at
2pm. *We'll continue with the normal schedule after that, so the one
after that will be February 9.
best regards,
Tuuli
Action items:
- Tuuli:
Set up a call for next week to discuss imputation details with
Natalja, Micha, Tim.
Continue masked mapping tests
- Esther, Peter, Natalja:
Send an outline of you miRNA analysis pipeline to the analysis
group mailing list
- Everyone:
Think and discuss in your lab about the analyses that you'd want to
do (lead and/or participate) with this dataset, by the next call
- Micha:
Continue mapping tests
- *Attending:* Tuuli, Micha, Esther, Ivo, Tim, Thomas x2, Mathias,
Peter, Olof, Matthias, Natalja
- *Sequencing:* Most of the labs will be able to meet the initial
deadline of Feb 15 despite the delays in kit delivery, which is great.
We agreed to keep the very last deadline of March 15; all the samples
and reruns should be done and data submitted by then.
- *Genotypes*: We need to impute about 40 samples that are not in 1000g
Phase 1 (they have Omni 2.5M haplotypes). Natalia/EBI could probably do
this, and Tuuli, Micha and Tim & co. want to be involved/informed too.
This should be done within a month.
- *miRNA analysis pipeline*: The labs who have experience of miRNA
analysis will send around details of how they map and quantify miRNAs.
We'll discuss on the next call how we should analyze them.
- *A new collaboration:* Mark McMarthy from Oxford is a long-term
collaborator of Manolis. They've developed a new kind of a burden test
to look at rare variant effects, and expressed interest in doing some
analysis with the Geuvadis data. People were positive about this, and
Mark's postdoc Manuel Rivas will present their plans in a future TC.
- *Analysis plans*: Tuuli would like to coordinate the future analyses
so that the essentials get done and there's no unnecessary overlaps. For
this we also need to assign people who will lead/participate/be informed
for each set of analysis. In the next call we'll start putting together
a list of what will be done and by whom.
- *Analysis group face-to-face meeting*: It would be good to get
together to discuss in real life once the data is ready and gone through
basic pipelines - maybe around April.
- *mRNA mapping*: The GEM paper will be submitted soon, so we might want
to use Micha's pipeline for mapping, quantification and normalization as
the basic approach. Micha presented some slides about an approach that
they're developing for SNP calling from RNAseq data, based on excessive
mapping. Tuuli presented results suggesting that reference allele
mapping bias affects exon quantifications. We should correct for it e.g.
by mapping to a masked reference.
--
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
12 Jan
12 Jan
5:27 p.m.
Dear all
As I said I will not be able to attend the calls at this day and time.
Jean Monlong from my group will bea ttending. He actually attended today
as well
Roderic
Dear all,
Here are minutes of the Geuvadis analysis group TC on January 12.
The next call has to be pushed forward by one week to *February 2 at
2pm. *We'll continue with the normal schedule after that, so the one
after that will be February 9.
best regards,
Tuuli
Action items:
- Tuuli:
Set up a call for next week to discuss imputation details with
Natalja, Micha, Tim.
Continue masked mapping tests
- Esther, Peter, Natalja:
Send an outline of you miRNA analysis pipeline to the analysis
group mailing list
- Everyone:
Think and discuss in your lab about the analyses that you'd want
to do (lead and/or participate) with this dataset, by the next call
- Micha:
Continue mapping tests
- *Attending:* Tuuli, Micha, Esther, Ivo, Tim, Thomas x2, Mathias,
Peter, Olof, Matthias, Natalja
- *Sequencing:* Most of the labs will be able to meet the initial
deadline of Feb 15 despite the delays in kit delivery, which is great.
We agreed to keep the very last deadline of March 15; all the samples
and reruns should be done and data submitted by then.
- *Genotypes*: We need to impute about 40 samples that are not in
1000g Phase 1 (they have Omni 2.5M haplotypes). Natalia/EBI could
probably do this, and Tuuli, Micha and Tim & co. want to be
involved/informed too. This should be done within a month.
- *miRNA analysis pipeline*: The labs who have experience of miRNA
analysis will send around details of how they map and quantify miRNAs.
We'll discuss on the next call how we should analyze them.
- *A new collaboration:* Mark McMarthy from Oxford is a long-term
collaborator of Manolis. They've developed a new kind of a burden test
to look at rare variant effects, and expressed interest in doing some
analysis with the Geuvadis data. People were positive about this, and
Mark's postdoc Manuel Rivas will present their plans in a future TC.
- *Analysis plans*: Tuuli would like to coordinate the future analyses
so that the essentials get done and there's no unnecessary overlaps.
For this we also need to assign people who will lead/participate/be
informed for each set of analysis. In the next call we'll start
putting together a list of what will be done and by whom.
- *Analysis group face-to-face meeting*: It would be good to get
together to discuss in real life once the data is ready and gone
through basic pipelines - maybe around April.
- *mRNA mapping*: The GEM paper will be submitted soon, so we might
want to use Micha's pipeline for mapping, quantification and
normalization as the basic approach. Micha presented some slides about
an approach that they're developing for SNP calling from RNAseq data,
based on excessive mapping. Tuuli presented results suggesting that
reference allele mapping bias affects exon quantifications. We should
correct for it e.g. by mapping to a masked reference.
--
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
--
(1) Centre de Regulacio Genomica
(2) Universitat Pompeu Fabra
Dr. Aiguader, 88 +34 93 3160110 ph
E-08003 Barcelona +34 93 3969983 fax
email: roderic.guigo(a)crg.cat http://big.crg.cat
RECOMB 2012 in Barcelona, http://recomb2012.crg.cat/
10 PhD fellowships, http://www.crg.eu/lacaixa_fellowships
3 fellowships for interdisciplinary post-doctoral studies
http://www.crg.es/interpod
13 Jan
13 Jan
8:24 a.m.
Dear all
Our miRNA pipeline was published in 2010 and is attached. One of the main features which
it does differently from the competitors is that it does properly annotate the mature and
star sequences of a miRNA and we have seen that they can behave very differently so it is
a shame to just summarize those. Moreover, it produces some nice output with counts for
each miRNA and other annotated small RNAs in a file that you can just open in Excel
On another note: Irina, my PhD student, also joined the call
Best wishes
Peter
________________________________
From: geuvadis_rna_analysis-bounces(a)lists.crg.es
[mailto:geuvadis_rna_analysis-bounces@lists.crg.es] On Behalf Of Tuuli Lappalainen
Sent: Thursday, January 12, 2012 4:31 PM
To: geuvadis_rna_analysis(a)lists.crg.es
Subject: [Geuvadis_rna_analysis] Geuvadis analysis group TC minutes
Dear all,
Here are minutes of the Geuvadis analysis group TC on January 12.
The next call has to be pushed forward by one week to February 2 at 2pm. We'll
continue with the normal schedule after that, so the one after that will be February 9.
best regards,
Tuuli
Action items:
- Tuuli:
Set up a call for next week to discuss imputation details with Natalja, Micha, Tim.
Continue masked mapping tests
- Esther, Peter, Natalja:
Send an outline of you miRNA analysis pipeline to the analysis group mailing list
- Everyone:
Think and discuss in your lab about the analyses that you'd want to do (lead
and/or participate) with this dataset, by the next call
- Micha:
Continue mapping tests
- Attending: Tuuli, Micha, Esther, Ivo, Tim, Thomas x2, Mathias, Peter, Olof, Matthias,
Natalja
- Sequencing: Most of the labs will be able to meet the initial deadline of Feb 15 despite
the delays in kit delivery, which is great. We agreed to keep the very last deadline of
March 15; all the samples and reruns should be done and data submitted by then.
- Genotypes: We need to impute about 40 samples that are not in 1000g Phase 1 (they have
Omni 2.5M haplotypes). Natalia/EBI could probably do this, and Tuuli, Micha and Tim &
co. want to be involved/informed too. This should be done within a month.
- miRNA analysis pipeline: The labs who have experience of miRNA analysis will send around
details of how they map and quantify miRNAs. We'll discuss on the next call how we
should analyze them.
- A new collaboration: Mark McMarthy from Oxford is a long-term collaborator of Manolis.
They've developed a new kind of a burden test to look at rare variant effects, and
expressed interest in doing some analysis with the Geuvadis data. People were positive
about this, and Mark's postdoc Manuel Rivas will present their plans in a future TC.
- Analysis plans: Tuuli would like to coordinate the future analyses so that the
essentials get done and there's no unnecessary overlaps. For this we also need to
assign people who will lead/participate/be informed for each set of analysis. In the next
call we'll start putting together a list of what will be done and by whom.
- Analysis group face-to-face meeting: It would be good to get together to discuss in real
life once the data is ready and gone through basic pipelines - maybe around April.
- mRNA mapping: The GEM paper will be submitted soon, so we might want to use Micha's
pipeline for mapping, quantification and normalization as the basic approach. Micha
presented some slides about an approach that they're developing for SNP calling from
RNAseq data, based on excessive mapping. Tuuli presented results suggesting that reference
allele mapping bias affects exon quantifications. We should correct for it e.g. by mapping
to a masked reference.
--
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>
6:43 p.m.
Dear all,
Our pipeline is basically as Peter's, the additions are a table of
isomirs counts and we also run miRDeep for novel miRNA discovery.
Best,
Esther
On 1/13/12 8:24 AM, P.A.C._t_Hoen(a)lumc.nl wrote:
Dear all
Our miRNA pipeline was published in 2010 and is attached. One of the
main features which it does differently from the competitors is that
it does properly annotate the mature and star sequences of a miRNA and
we have seen that they can behave very differently so it is a shame to
just summarize those. Moreover, it produces some nice output with
counts for each miRNA and other annotated small RNAs in a file that
you can just open in Excel
On another note: Irina, my PhD student, also joined the call
Best wishes
Peter
------------------------------------------------------------------------
*From:*geuvadis_rna_analysis-bounces@lists.crg.es
[mailto:geuvadis_rna_analysis-bounces@lists.crg.es] *On Behalf Of
*Tuuli Lappalainen
*Sent:* Thursday, January 12, 2012 4:31 PM
*To:* geuvadis_rna_analysis(a)lists.crg.es
*Subject:* [Geuvadis_rna_analysis] Geuvadis analysis group TC minutes
Dear all,
Here are minutes of the Geuvadis analysis group TC on January 12.
The next call has to be pushed forward by one week to *February 2 at
2pm. *We'll continue with the normal schedule after that, so the one
after that will be February 9.
best regards,
Tuuli
Action items:
- Tuuli:
Set up a call for next week to discuss imputation details with
Natalja, Micha, Tim.
Continue masked mapping tests
- Esther, Peter, Natalja:
Send an outline of you miRNA analysis pipeline to the analysis
group mailing list
- Everyone:
Think and discuss in your lab about the analyses that you'd want
to do (lead and/or participate) with this dataset, by the next call
- Micha:
Continue mapping tests
- *Attending:* Tuuli, Micha, Esther, Ivo, Tim, Thomas x2, Mathias,
Peter, Olof, Matthias, Natalja
- *Sequencing:* Most of the labs will be able to meet the initial
deadline of Feb 15 despite the delays in kit delivery, which is great.
We agreed to keep the very last deadline of March 15; all the samples
and reruns should be done and data submitted by then.
- *Genotypes*: We need to impute about 40 samples that are not in
1000g Phase 1 (they have Omni 2.5M haplotypes). Natalia/EBI could
probably do this, and Tuuli, Micha and Tim & co. want to be
involved/informed too. This should be done within a month.
- *miRNA analysis pipeline*: The labs who have experience of miRNA
analysis will send around details of how they map and quantify miRNAs.
We'll discuss on the next call how we should analyze them.
- *A new collaboration:* Mark McMarthy from Oxford is a long-term
collaborator of Manolis. They've developed a new kind of a burden test
to look at rare variant effects, and expressed interest in doing some
analysis with the Geuvadis data. People were positive about this, and
Mark's postdoc Manuel Rivas will present their plans in a future TC.
- *Analysis plans*: Tuuli would like to coordinate the future analyses
so that the essentials get done and there's no unnecessary overlaps.
For this we also need to assign people who will lead/participate/be
informed for each set of analysis. In the next call we'll start
putting together a list of what will be done and by whom.
- *Analysis group face-to-face meeting*: It would be good to get
together to discuss in real life once the data is ready and gone
through basic pipelines - maybe around April.
- *mRNA mapping*: The GEM paper will be submitted soon, so we might
want to use Micha's pipeline for mapping, quantification and
normalization as the basic approach. Micha presented some slides about
an approach that they're developing for SNP calling from RNAseq data,
based on excessive mapping. Tuuli presented results suggesting that
reference allele mapping bias affects exon quantifications. We should
correct for it e.g. by mapping to a masked reference.
--
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University ofGeneva Medical School
CMU / Rue Michel-Servet 1
1211Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch>
31 Jan
31 Jan
5 p.m.
Dear all,
Our miRNA pipeline "Kraken" is in publication process now. Draft and
diagram are in attachment.
Regards,
Natalja
On 13/01/12 07:24, P.A.C._t_Hoen(a)lumc.nl wrote:
Dear all
Our miRNA pipeline was published in 2010 and is attached. One of the
main features which it does differently from the competitors is that
it does properly annotate the mature and star sequences of a miRNA and
we have seen that they can behave very differently so it is a shame to
just summarize those. Moreover, it produces some nice output with
counts for each miRNA and other annotated small RNAs in a file that
you can just open in Excel
On another note: Irina, my PhD student, also joined the call
Best wishes
Peter
------------------------------------------------------------------------
*From:*geuvadis_rna_analysis-bounces@lists.crg.es
[mailto:geuvadis_rna_analysis-bounces@lists.crg.es] *On Behalf Of
*Tuuli Lappalainen
*Sent:* Thursday, January 12, 2012 4:31 PM
*To:* geuvadis_rna_analysis(a)lists.crg.es
*Subject:* [Geuvadis_rna_analysis] Geuvadis analysis group TC minutes
Dear all,
Here are minutes of the Geuvadis analysis group TC on January 12.
The next call has to be pushed forward by one week to *February 2 at
2pm. *We'll continue with the normal schedule after that, so the one
after that will be February 9.
best regards,
Tuuli
Action items:
- Tuuli:
Set up a call for next week to discuss imputation details with
Natalja, Micha, Tim.
Continue masked mapping tests
- Esther, Peter, Natalja:
Send an outline of you miRNA analysis pipeline to the analysis
group mailing list
- Everyone:
Think and discuss in your lab about the analyses that you'd want
to do (lead and/or participate) with this dataset, by the next call
- Micha:
Continue mapping tests
- *Attending:* Tuuli, Micha, Esther, Ivo, Tim, Thomas x2, Mathias,
Peter, Olof, Matthias, Natalja
- *Sequencing:* Most of the labs will be able to meet the initial
deadline of Feb 15 despite the delays in kit delivery, which is great.
We agreed to keep the very last deadline of March 15; all the samples
and reruns should be done and data submitted by then.
- *Genotypes*: We need to impute about 40 samples that are not in
1000g Phase 1 (they have Omni 2.5M haplotypes). Natalia/EBI could
probably do this, and Tuuli, Micha and Tim & co. want to be
involved/informed too. This should be done within a month.
- *miRNA analysis pipeline*: The labs who have experience of miRNA
analysis will send around details of how they map and quantify miRNAs.
We'll discuss on the next call how we should analyze them.
- *A new collaboration:* Mark McMarthy from Oxford is a long-term
collaborator of Manolis. They've developed a new kind of a burden test
to look at rare variant effects, and expressed interest in doing some
analysis with the Geuvadis data. People were positive about this, and
Mark's postdoc Manuel Rivas will present their plans in a future TC.
- *Analysis plans*: Tuuli would like to coordinate the future analyses
so that the essentials get done and there's no unnecessary overlaps.
For this we also need to assign people who will lead/participate/be
informed for each set of analysis. In the next call we'll start
putting together a list of what will be done and by whom.
- *Analysis group face-to-face meeting*: It would be good to get
together to discuss in real life once the data is ready and gone
through basic pipelines - maybe around April.
- *mRNA mapping*: The GEM paper will be submitted soon, so we might
want to use Micha's pipeline for mapping, quantification and
normalization as the basic approach. Micha presented some slides about
an approach that they're developing for SNP calling from RNAseq data,
based on excessive mapping. Tuuli presented results suggesting that
reference allele mapping bias affects exon quantifications. We should
correct for it e.g. by mapping to a masked reference.
--
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University ofGeneva Medical School
CMU / Rue Michel-Servet 1
1211Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch>
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Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
--
Natalja Kurbatova, PhD
Functional Genomics Group, EBI
5026
days inactive
5045
days old
geuvadis_rna_analysis@lists.crg.es
4 comments
5 participants
participants (5)
-
Esther Lizano -
Natalja Kurbatova -
P.A.C._t_Hoen＠lumc.nl -
Roderic Guigo -
Tuuli Lappalainen