Minutes RNA-Seq Analysis group (2013-11-05 15:00-16:00) == Participants == * Peter-Bram 't Hoen (LUMC) * Michiel van Galen (LUMC) * Martijn Vermaat (LUMC) * Wibowo Arindrarto (LUMC) * Jeroen van Rooij (EMC) * Lude Franke (UMCG) * Patrick Deelen (UMCG) * Freerk van Dijk (UMCG) * Dasha Zhernakova (UMCG) * Rick Jansen (VUMC) == Data Generation and Upload == * SRM was down last week, 240 samples are ready to send in Rotterdam, this will be send when the SRM is back online. * '''Martijn will''' contact the people in Utrecht for their genotype data, so we can continue with these analyses once the samples are uploaded. * '''Wibowo will''' create a zipfile of the quantifications for easy access. Michiel/Wibowo should be contacted to add any other tools/analysis to the grid. This is in progress, after the SRM is gets back online. The links to access them are available here: http://www.bbmriwiki.nl/wiki/FgPipelineOutput/5ddcae7 == QC Issues == * Jeroen will look into the QC-metrics generated from the first 2300 samples. * Peter-Bram will look into pairwise correlations. * Lude asked if any cohorts have more details on the cell counts, Martijn will look into this. == Pipeline on the Grid == * Since the SRM was down it's difficult to run some analysis, it might be useful to have a backup for the pipeline, Dasha will look into using the Groningen server for this. * To run more tools on the grid/VM, we can contact Michiel to get started. Michiel/Dasha will try to get SNVmix running on the grid (Martijn will join them because he might want to get some tools running there too) == Update on e/splice/trans/polyA-QTL analyses == * No update on the eQTL analyses at the moment, there was an issue with the amount of disk space on the VM, this was known and should be resolved this week. * Peter-Bram talked with Renee about spliceQTLs, she will write some ideas down by the end of this week. * Peter-Bram obtained list of sites known to be troublesome in eQTL analysis == Any Other Business == * Maarten has joined the call today, he will be working mostly on Methylation data at the LUMC * On the RNA-course in Leiden last week, somebody from outside offered to help in this project, Lude will contact this person Next call is on Tuesday 12-11-2013 at 15:00.