[Geuvadis_rna_analysis] Geuvadis analysis group TC May 24th - Minutes

Hello, Here are the minutes of the TC. The next call will in *in two weeks, June 7th at 2pm CET*. - Discussion about the wiki - the current system is not necessarily the best, but we'll stick to it. We might want to consider making at least part of the wiki public after the paper is out, but this is to be decided later. - Gabrielle will install the EtherPad shared writing tool (pretty similar to GoogleDocs but will work with our wiki user IDs). This will be good for writing and editing documents (e.g. the eventual manuscript draft) as a group, and can be used also otherwise when a more interactive writing tool than the wiki is needed. - Natalja has discussed data visualization using the Ensembl browser, and will create a test site. Tuuli will check options for eQTL and ASE results browsing/visualization. - Abstracts for ASHG: Tuuli will submit the main project abstract, but subprojects abstracts are also possible. Manny is planning to submit one of LoF analyses; others please send an email to the analysis list if you're planning to submit something. A QC abstract might be a good idea. Deadline is on June 4th. - The GEM manuscript has been submitted, so we'll start switching everything to GEM now. The bams are available on the ftp site, Tuuli has downloaded them and is processing them now. Transcript quantifications based on GEM+flux are already available. There will be some updates on the file names to keep everything consistent, so you might want to wait a few days before downloading. - Tuuli has created a wiki page for storing all specifications of identifiers and file formats. Everyone should follow these specs, and update them as necessary (send an email to the analysis if/when there are modifications). - There was some discussion on the LoF subgroup call whether we should switch to Gencode v12 after all, but it would be a lot of work - we'll stick to v7. - We might want to revise the variant annotation format for the v2 of annotations, the current one (that mostly follows VAT) is difficult to parse. Tuuli will create an EtherPad document for putting this together. - Manny presented slides of LoF analyses - annotations, analysis plans, early results - everything looks good. 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(a)unige.ch On 5/24/12 10:28 AM, Tuuli Lappalainen wrote: