Hello,

Here are the minutes of the Geuvadis RNAseq analysis group call.

The next analysis group call will be on February 23 at 2pm, but don't forget the general RNAseq call on February 14 at 4pm.

- sequencing is running as it should
- the analysis group meeting will be held in Geneva on April 16-17
- imputation is finished, and next week Natalja will produce a vcf file. We'll include all the variants without initial quality filter, with a clear indication that the genotypes needs QC before using it for anything.
- Micha has ran his quantification pipeline for the first round of sequencing from Geneva. He'll upload all the transcript quantifications and bam files of the sandbox 24 to the ftp site, and run exon quantifications for the 24 samples too
- Tuuli will finish her analysis of allelic bias in mapping by the next call
- we discussed small RNA QC. Tuuli's first results of 5 test samples didn't look very good, with a nonoptimal size distribution and <10% mapping to mature miRNA sequences. Natalja and Barcelona will email more detailed QC results soon. In Peter's opinion we should be able to do some analysis even with these data. We'll be in email contact during the next few days to come up with simple QC steps for all the labs, and discuss next actions on the main RNAseq TC call on the 12th.
- Manuel Rivas from Oxford presented slides about his plans for loss-of-function variant analysis, including detection of unannotated splice variants and NMD patterns, and we discussed various ways to approach these issues. At least Micha and Tuuli will be involved in these analyses.

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@unige.ch

On 2/8/12 6:23 PM, Tuuli Lappalainen wrote:
Hello all,

We have the Geuvadis analysis group TC on Thursday (Feb 8) at 2pm.

On the agenda:
- updates on sequencing if needed
- analysis group face-to-face meeting
    Please fill the Doodle! http://www.doodle.com/24a4i3n8bkynhpwx
- small RNA QC
- Manuel Rivas will present some slides on LOF analysis plans


Here are the call details:

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@unige.ch


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