13 Dec
2011
13 Dec
'11
11:27 a.m.
Hi all,
We'll have the Geuvadis RNAseq analysis group TC today at 3pm, we should
receive the details from Barcelona soon.
On the agenda:
- updates on sequencing and protocols (if needed)
- low-level data processing: whose pipeline to use
Micha and Natalja, we discussed that you would be interested in doing
mapping and quantification of this dataset. I hope you can attend the
call - and could you please send a summary of the methods that your
pipeline uses so that we can discuss this on the call?
Here's what we could do in Geneva: normally we use bwa for mapping
(which maps 10%+ reads compared to Tophat), and Geuvadis data we would
probably map first to the genome, and nonmapping reads then to the
transcriptome. This should yield exonic mapping of ~60% of the reads.
Quantifications we do as a standard at the exon level, by simply
counting all the reads that overlap an exon. We have some more complex
alternatives as well, but for eQTL analysis we prefer to use these exon
quantifications. Regarding normalization, we're in the process of
developing our current methods further and would use the most up to date
method that we have, but I don't have the details yet. Another thing
that we'd need to take into account is reference allele mapping bias,
which affects exon quantifications a little bit as well. bwa doesn't
allow masking but we can deal with it in other ways - but I'd like to
run mapping also with a software that allows masking (Tophat, GEM??).
Talk to you later,
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
-------- Original Message --------
Subject: Geuvadis RNAseq analysis group TC
Date: Wed, 07 Dec 2011 20:38:36 +0100
From: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch>
To: geuvadis_rna_analysis(a)lists.crg.es
Hi all,
Thanks for the quick replies to the doodle about the Geuvadis analysis
group TCs. It seems that *Thursday 2pm CET* is the best time, so please
keep that slot free for next spring. Let's have calls every 2 weeks by
default, starting on January 12.
But we should have one call before Christmas and start with an exception
since next week's Thursday is impossible for me. So let's have a TC on
*Tuesday December 13th at 3pm*. As I said before, those who want to do
mapping etc. to the raw data should send an email with a brief
description of their pipeline before the call.
cheers,
Tuuli
PS. Marta, I'm sorry that I had to pick a time that wasn't good for you
- the other times would have had even more people missing. I hope you
can join at least sometimes or find someone else who could attend the
call instead.
--
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