Hello all,

Here are the minutes of last week's Geuvadis RNAseq analysis group TC - sorry for the delay.

- the next call will be on March 9th.
- mRNA sequencing: done in all the labs except for ~15 samples in total that need a rerun. A couple of labs have already uploaded the fastqs on the ftp site, and the rest promised to do so during the following week.
- miRNA sequencing: needs a bit more time still - a couple of labs are done, a few are sequencing them during the following week, and some labs need to rerun to get more coverage.
- miRNA dropouts: it will be very difficult in practice for many labs to rerun individual dropouts. We decided that it's best to just ignore these samples and absorb the slight reduction in sample size - sending libraries to other labs would be too difficult.
- analysis group meeting in Geneva 16-17 April: Tuuli will send further info about practicalities. Everyone who is involved in the RNAseq project is welcome to attend.
- genotypes: Imputation is done, and Natalja is building the vcf files. Should be finished within a week.
- miRNA analysis pipeline: Natalja promised to run the EBI pipeline to quantify miRNAs, and Barcelona will also run theirs to quantify and look at isomirs.
- mRNA analysis pipeline: Micha's pipeline will be used to quantify transcripts, and he'll present some further details of GEM+flux on a future call. We should also get just simple read counts in exons - Tuuli can run this in Geneva, probably based on mapping with GEM.
- Tuuli presented slides about the effect of genetic variants on mapping. In mapping to the standard genome there is often some reference allele bias, that could cause some false positives. Based on Tuuli's simulations, this is unlikely to be hugely common in mRNAseq, but very frequent in miRNAs. Tuuli has a pipeline to find variants that can lead to mapping biases, and approaches to filter/correct for this in quantifications and ASE analysis.

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 2/23/12 11:37 AM, Tuuli Lappalainen wrote:
Dear all,

We'll have our Geuvadis RNAseq analysis group call again today (Thursday) at 2pm.

Things to be discussed:
- update on sequencing progress
- miRNA QC issues
- Tuuli will present some slides on how genetic variants affect mapability, and ways to correct for it
- mRNA and miRNA data processing pipelines



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