= Minutes RNA-Seq Analysis group (2013-11-12 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)
 * Rick Jansen (VUMC)
 * Renee (VUMC)
 
== Data Generation and Upload == 
 * Second batch was uploaded to the grid containing more of the Amsterdam Samples. These will be processed on the grid as soon as possible.
 * Wibowo uploaded the QC-metrics and the genecounts on thi grid and the wiki: http://www.bbmriwiki.nl/wiki/FgPipelineOutput/5ddcae7.
 
== QC Issues ==
 * Jeroen emailed some plots on the general QC-metrics, these were discussed during the call. We noticed the first batch of Amsterdam samples were behaving different then the other samples, the second batch should be added to these QC-metrics.
 * Martijn will look into the high amount of duplicate reads in some samples, to evaluate what is going on there.
 * Peter-Bram and Lude ran some other QC-checks, the data of these various efforts should be compared to determine and understand the outliers.

== Pipeline on the Grid ==
 * Michiel is working with Dasha and Martijn to get other tools working on the grid.
 
== Update on e/splice/trans/polyA-QTL analyses ==
 * Lude is running the eQTL analysis on the VMcloud on the full set of samples.
 * Renee provided an update on the spliceQTL analysis, she is using the Geuvadis dataset as a pilot and will apply those methods on our data later.
 * Martijn is getting started on the grid for his analysis to polyA-QTL analysis.

== Allele Specific Expression ==
 * Lude ran some analysis on the Guevadis data, which looked promising, and will provide a further update next week. 
 
== Wiki ==
 * Use the Fg when you start a new page so it isn't publicly available.
 * Should be used to put the methods and (small) results so the others can work with it.
 
== Any Other Business ==
 * Renee has joined the call today, She will be working on the data-analysis.
 * Cleanup on the SRM, everybody who has data there should have a look at their data to move it (see email Leon)
 * Shared directory on the VMcloud for reference files.
 
Next call is on Tuesday 19-11-2013 at 15:00.