| | 1 | = Minutes RNA-Seq Analysis group (2013-11-12 15:00-16:00) = |
| | 2 | |
| | 3 | == Participants == |
| | 4 | * Peter-Bram 't Hoen (LUMC) |
| | 5 | * Michiel van Galen (LUMC) |
| | 6 | * Martijn Vermaat (LUMC) |
| | 7 | * Wibowo Arindrarto (LUMC) |
| | 8 | * Jeroen van Rooij (EMC) |
| | 9 | * Lude Franke (UMCG) |
| | 10 | * Rick Jansen (VUMC) |
| | 11 | * Renee (VUMC) |
| | 12 | |
| | 13 | == Data Generation and Upload == |
| | 14 | * Second batch was uploaded to the grid containing more of the Amsterdam Samples. These will be processed on the grid as soon as possible. |
| | 15 | * Wibowo uploaded the QC-metrics and the genecounts on thi grid and the wiki: http://www.bbmriwiki.nl/wiki/FgPipelineOutput/5ddcae7. |
| | 16 | |
| | 17 | == QC Issues == |
| | 18 | * 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. |
| | 19 | * Martijn will look into the high amount of duplicate reads in some samples, to evaluate what is going on there. |
| | 20 | * Peter-Bram and Lude ran some other QC-checks, the data of these various efforts should be compared to determine and understand the outliers. |
| | 21 | |
| | 22 | == Pipeline on the Grid == |
| | 23 | * Michiel is working with Dasha and Martijn to get other tools working on the grid. |
| | 24 | |
| | 25 | == Update on e/splice/trans/polyA-QTL analyses == |
| | 26 | * Lude is running the eQTL analysis on the VMcloud on the full set of samples. |
| | 27 | * 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. |
| | 28 | * Martijn is getting started on the grid for his analysis to polyA-QTL analysis. |
| | 29 | |
| | 30 | == Allele Specific Expression == |
| | 31 | * Lude ran some analysis on the Guevadis data, which looked promising, and will provide a further update next week. |
| | 32 | |
| | 33 | == Wiki == |
| | 34 | * Use the Fg when you start a new page so it isn't publicly available. |
| | 35 | * Should be used to put the methods and (small) results so the others can work with it. |
| | 36 | |
| | 37 | == Any Other Business == |
| | 38 | * Renee has joined the call today, She will be working on the data-analysis. |
| | 39 | * Cleanup on the SRM, everybody who has data there should have a look at their data to move it (see email Leon) |
| | 40 | * Shared directory on the VMcloud for reference files. |
| | 41 | |
| | 42 | Next call is on Tuesday 19-11-2013 at 15:00. |
| | 43 | |
