2 May
2012
2 May
'12
2:56 p.m.
Dear all,
Here are the minutes of last week's Geuvadis RNAseq call.
best regards,
Tuuli
Geuvadis RNAseq Teleconference April 26, 2012 Minutes
Written by Tuuli L.
-Tuuli gave an update on the data
omRNA
§Fastqs are all OK, and there's a freeze folder on the ftp site. Natalja
should change the write access so that only her and Tuulican modify the
content of that folder.
§There are no sample swaps in the data, but 5 samples show increased
heterozygosity in RNAseq data suggesting some cross-contamination. These
samples are included in the fastq freeze but will be excluded from the
analysis. Tuuli has flagged them in all possible READMEs.
§The data has been mapped both with bwa and GEM. The latter gives better
results, and if the GEM manuscript is submitted very soon, it will be
the mapper to use in this project. Tuuli's analysis for the CSHL poster
is based on bwa due to time constraints.
§Data quality seems excellent: lab effects are not a major problem
omiRNA
§Sequencing data of the last 48 samples from Kiel are still missing, but
the fastqs will be uploaded probably within 2 weeks but certainly by the
end of May
§Marc F. has been running this pipeline for miRNA QC and quantification,
results to expect very soon
oGenotypes
§Imputation of the ~40 1000g Phase2 samples has some issues. This has to
be sorted out soon.
-Discussion on whether we should aim to publish a separate QC paper
before the main paper. The consensus was not to do this.
-The analysis group meeting in Geneva in April 16-17 was very productive
and people enjoyed it. The next meeting will be in Barcelona in the end
of June or early July; everyone involved in analysis is welcome to attend.
-Tuuli presented the analysis plan that was put together by the analysis
group in Geneva. Some minor additions.
-Discussion about collaborations with members of the 1000g analysis
group: Kai Ye (Leiden) from the structural variation group would like to
look into effects of CNVs, and we'll discuss with him in more detail how
he'd contribute. Daniel McArthur (Boston) from the functional
interpretation group will be involved in loss-of-function analysis.
-Deadline for any analysis for the CSHL poster is May 1^st , but anyone
planning to contribute should let Tuuli know in advance
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 4/25/12 11:41 PM, Tuuli Lappalainen wrote:
Dear all,
We will have a Geuvadis RNAseq call for the whole group on Thursday at
11am CET. I hope many of you can attend; the details and the agenda
are below.
I will present the analysis plan that we drafted at the analysis group
meeting last week, see the attachment. I also attached an outline of
the analyses that I'm planning to include in the Biology of Genomes
poster.
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 4/19/12 5:37 PM, Gabrielle Anne Bertier wrote:
>
> Dear All, thank you very much for filling in the doodle.
>
> We'll have the next TC on *_Thursday 26th April at 11am_*
>
> Date and time
>
>
>
> *Thursday 26th April at 11am*
>
> Ready-Access Number:
>
>
>
> 900800678
>
> Secondary Ready-Access Number:
>
>
>
> +34 917911859
>
> 7-Digit Access Code:
>
>
>
> 3160100
>
> Tentative agenda:
>
> - status of the data
>
> - updates from the analysis group meeting
>
> - analysis plans
>
> - Biology of Genomes poster draft
>
> - future meetings
>
> The next Analysis meeting will take place in Barcelona and anyone
> interested is welcome to join,
>
> here is the doodle for the next meeting:
> http://www.doodle.com/z7a3mq92b9syz9xg
>
> Conference code:
>
> Best,
>
> Tuuli and Gabrielle
>
> */Gabrielle Bertier/*
>
> /Scientific Project Manager
> International Collaboration Office
> CRG, Center for Genomic Regulation
> Carrer Dr. Aiguader, 88/
>
> /08003 Barcelona, España
> /Tel: +34933160374
> Mobile: +34639960656
> email: gabrielle.bertier(a)crg.es <mailto:gabrielle.bertier@crg.es>
>
> web:www.geuvadis.eu
>
> *From:*geuvadis_wpl-bounces@lists.crg.es
> [mailto:geuvadis_wpl-bounces@lists.crg.es] *On Behalf Of *Tuuli
> Lappalainen
> *Sent:* 17 April, 2012 5:22 PM
> *Cc:* geuvadis_rnaseq(a)lists.crg.es; geuvadis_wpl(a)lists.crg.es
> *Subject:* Re: [Geuvadis_wpl] GEUVADIS RNAseq General Update
>
> Dear all,
>
> Please fill in the Doodle for a TC with the whole Geuvadis RNAseq
> group by Wednesday noon.
>
> 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 <mailto:tuuli.lappalainen@unige.ch>
>
>
> On 4/12/12 11:10 AM, Gabrielle Anne Bertier wrote:
>
> Dear all,
>
> At the request of Tuuli, please fill in the doodle
> <http://doodle.com/3i5f4wt28ez596sx> to schedule a TC with the whole
> RNAseq group for an update on the data analysis.
>
> Tentative agenda:
>
> - status of the data
>
> - updates from the analysis group meeting
>
> - analysis plans
>
> - Biology of Genomes poster draft
>
> - future meetings
>
> Kind regards,
>
> Gabrielle
>
> doodle full link: http://doodle.com/3i5f4wt28ez596sx
>
> */Gabrielle Bertier/*
>
> /Scientific Project Manager
> International Collaboration Office
> CRG, Center for Genomic Regulation
> Carrer Dr. Aiguader, 88/
>
> /08003 Barcelona, España
> /Tel: +34933160374
> Mobile: +34639960656
> email: gabrielle.bertier(a)crg.es <mailto:gabrielle.bertier@crg.es>
>
> web:www.geuvadis.eu
>
>
>
>
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