Dear all,
The Geuvadis RNAseq paper was rejected this morning. We've decided
with Manolis that we should make an appeal, and we have already been
in touch with Magdalena about this. We'll need to send her a
response letter in a couple of days (see the attachment with
reviewer's comments and a rough response draft). It ain't over til
it's over.
Since we were going to have a call soon anyway, let's have a TC
on Thursday the 24th at 4pm CET. Before that, I'd be happy to
hear your comments to the response letter (deadline:
immediately). There's a couple of bigger items to discuss, and
specific questions to a few of you - see below. There won't be a lot
of new analysis to do if we're given the chance to revise.
Questions:
- Do we drop non-essential analyses as #2 suggests? This would mean
RNA editing, maybe fusions and subtle splicing. I'm not keen to, but
if people think it would improve the overall quality of the paper...
- Should we restructure the supplement by topic instead of
methods/figures/tables? Need to ask Magdalena too.
- Andrew & Natalja: Can we add a data slicing and download
function to the browser (or a separate site linked from the
browser)?
- Jean & Mar: How is the qualitative/quantitative analysis
affected by low-abundance transcripts? Will the results change if
the threshold is different?
- Jean, Mar, Pedro, Micha (and myself): #2 raises an important
question (really!): most of transcript variation is explained by
transcript ratio differences, but we find very few QTLs for this.
Why do you think this is? Is all that variation really just
random/environmental/epigenetic?
- Jean: #3 suspects that the 3% of transcriptome variation explained
by population could be just random - how do we respond to this?
- Manny: What could we do to add novelty value to NMD analysis?
- Gabrielle: Is it possible to make a read-only password for the
wiki? We could give one to the reviewers just so that they can see
it.
best regards,
Tuuli
--
Tuuli Lappalainen, PhD
Department of Genetics, Stanford University School of Medicine , and
Department of Genetic Medicine and Development, University of Geneva
Email: tuuli.e.lappalainen@gmail.com / tlappala@stanford.edu
Tel: +1 415 351 9713
Bustamante lab
Department of Genetics
300 Pasteur Dr. Lane L301
Stanford, CA 94305-5120
USA