Hello,

Here are the minutes of the Geuvadis RNAseq analysis group TC. The next call will be on February 9 at 2pm.

- Sequencing is going well, and we're on schedule to keep the final deadline of March 15 for fastq uploads. 
- Tuuli will resend the instructions for data processing, file naming and ftp upload. These (as all other guidelines) can always be found from the wiki.
- We'll have a face-to-face meeting for the analysis group in mid-April. Please fill in the Doodle for the dates before the next call: http://www.doodle.com/24a4i3n8bkynhpwx . Geneva, Berlin and Leiden are volunteering to host, let's decide that next week.
- We'll submit an abstract for the Biology of Genomes meeting at Cold Spring Harbor in mid-May. Tuuli will circulate the abstract draft later.
- Marc from Berlin presented some slides of QC analysis of mRNAseq data, the main point being that the quality looks good and DNA contamination is not an issue.
- miRNA QC steps were discussed. Many of the labs don't have the experience and pipelines to do initial QC for the data that they produce. Tuuli will upload Geneva's miRNA fastq files to the ftp site so that people with more experience can take a look and define some basic QC criteria asap (I'm sorry but I forgot who promised to do this, can you send me an email?).
- The draft of analysis plans was discussed. It's been added to the wiki (analysis page), feel free to edit it further anytime.

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 2/2/12 1:08 PM, Tuuli Lappalainen wrote:


Hello all,

Here are the call details for today's TC:

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


-------- Original Message --------
Subject: Geuvadis RNAseq AG call on Thursday
Date: Tue, 31 Jan 2012 18:53:51 +0100
From: Tuuli Lappalainen <Tuuli.Lappalainen@unige.ch>
To: geuvadis_rna_analysis@lists.crg.es 


Hello all,

We'll have out next Geuvadis analysis group TC on Thursday January 2 at 
2pm.

Lots of things on the agenda:
- sequencing updates
- analysis group face-to-face meeting: time, duration, location
- abstract for the Biology of Genomes meeting at Cold Spring Harbor
- Marc will present results of the DNA contamination analysis
- miRNA data processing and QC
- analysis plans (see below)

As we discussed on the last call, I'd like to start putting together a 
plan of what we all eventually want to do with the data. The data is of 
course shared and everyone is free to do what they want, but we need to 
make sure that the essentials get done and that there's no unnecessary 
overlap. As a starting point for discussion, take a look at the analysis 
breakdown draft that I wrote 
(https://docs.google.com/document/d/1_LAkv0NGSrXU6LSsyhN_GnZB4WRanl-e993U_0IbxRE/edit), 
and feel free to edit it before/during the call.

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




_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis@lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis