Hi all,
Here are the minutes of last Thursdays conference call.
best regards,
Tuuli
Geuvadis analysis call TC Minutes, May 3 2012
The next call will be in 2 weeks, May 17 at 2pm CET.
Action items
- Coordinators of each analysis module should organize a wiki Analysis page. Ask Gabrielle if you need to rename existing pages or move them around
- Everyone should use the mailing list more for sharing results and also for questions so that information is better shared – avoid emails only to 1-2 people
- Micha et al will proceed with the gem->bam conversion
Discussion on use of the wiki.
- Each analysis module should have their own page (with children pages as necessary), and the person(s) responsible for each module should take care of organizing their own respective pages, and seeing that the content is up to date.
- When people add any significant information to the wiki, they should send an email with a link to the analysis group mailing list
- Gabrielle will see if the tags of recent changes could have more granularity – for now people should indicate the author in the text.
Discussion on use of the AG mailing list
- Tuuli suggested that we’d move the majority of email exchange to the analysis group mailing lists – now there’s a lot of email between 2-3 people, and Tuuli’s having hard time keeping track that all necessary information gets shared with all the relevant people (and deciding who the relevant people are in each case). From now on, please send questions and analysis results to the mailing list unless it’s a very technical issue concerning only a subset of people.
The next analysis group meeting will be on July 9-10 in Barcelona.
Tuuli presented the Biology of Genomes poster
Tuuli’s results (slides sent a few days before) of 5 samples showed that GEM is really superior to bwa – which is not surprising, but nice to see. If the GEM submission happens as planned, we’ll switch to GEM. Micha et al. are incorporating the latest GEM-BAM conversion to their pipeline and will run the conversions next week.
There’s been advance on the imputation front. We’re on track to having bams, transcript and exon quantifications and genotypes all ready for analysis by the end of May.
Micha will present the results that he sent around about gene discovery and RNA editing on the next call.
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
I'm not able to connect, the pin code doesn't work. Gabrielle, can you do something? Were the rest of you able to connect?
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 5/2/12 3:41 PM, Tuuli Lappalainen wrote:Hi all,
We'll have a Geuvadis RNAseq analysis group TC on Thursday May 3rd at 2pm.
On the agenda:
- Tuuli will present the Biology of Genomes poster
- Other analysis updates
- Steps needed to get a final freeze for analysis by the end of May
- Analysis group meeting in Barcelona
- Mailing lists
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
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