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@unige.ch
-------- Original Message --------
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@unige.ch
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