Esther and I were there also ! :)

From: geuvadis_rna_analysis-bounces@lists.crg.es [mailto:geuvadis_rna_analysis-bounces@lists.crg.es] On Behalf Of Tuuli Lappalainen
Sent: martes, 13 de diciembre de 2011 16:57
To: geuvadis_rna_analysis@lists.crg.es
Subject: [Geuvadis_rna_analysis] Geuvadis RNAseq analysis group TC minutes

Hello all,

A brief summary of the first analysis group TC. Action items in bold. Next call Thursday January 12, 2pm.

Attending: Tuuli, Micha, Natalja, Marc, Mathias, Tim, Olof, Marta

1) Kit situation
- Geneva and Barcelona have both mRNA and miRNA kits
- Berlin and Kiel have miRNA kits
- Munich, Uppsala and Leiden (?) don't have any kits
- All the labs should send Tuuli an update before Christmas indicating if they have received the kits or not. We'll wait until early January and see then if we need a plan B.
- the labs that have kits are on schedule with the sequencing

2) Low-level data processing (mapping, quantification etc.)
- Tuuli will upload the fastq files and bams (from bwa) from their mRNA seq by the end of the week.
- Tuuli will define a sandbox dataset of 24 and 5 samples from UNIGE for testing purposes.
- Micha will find out when GEM is likely to be published
- We shouldn't spend too much time figuring out how to map the reads - this has been done already. However, there are a couple of things that we should test:
- Marc will analyze the level of genomic contamination in the 24 samples
- Tuuli has concerns about reference allele mapping bias affecting quantifications. Natalja will run       Tophat for 5 samples with the normal reference (hg19) and a reference masked for all common 1000g variants (Tuuli will provide this) to see if masking leads to a big loss in mapping. Micha will check whether it's possible with GEM. If masking is not feasible, we can consider other options for dealing with this bias...

The following was planned for the final dataset:
- Micha will run his whole pipeline (GEM for mapping, SNAPE for variant calling, Flux for deconvolution and normalization, AStalavista for alternative splicing analyzes..).
- Natalja will run the EBI pipeline using bwa and/or tophat, and quantify exon counts and/or RPKMs. bwa+exon counts would enable direct comparison with earlier eQTL results from Manolis's lab
- regarding normalization, both PCA and specific covariate based approaches are possible - we'll have to see what the data looks like
- all analyses should be run with duplicates - Geneva has seen that in RNAseq data duplicates rarely seem to be PCR artefacts

3) FTP instructions
- Natalja will send an email to the analysis group about the FTP instructions that are now on the ftp site

I hope I remembered at least the most important things! I'll let you know when the data is one the ftp site.


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