| | 1 | Dasha: = Minutes RNA-Seq Analysis group (2013-11-05 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 | * Patrick Deelen (UMCG) |
| | 11 | * Freerk van Dijk (UMCG) |
| | 12 | * Dasha Zhernakova (UMCG) |
| | 13 | * Rick Jansen (VUMC) |
| | 14 | |
| | 15 | == Data Generation and Upload == |
| | 16 | * SRM was down last week, 240 samples are ready to send in Rotterdam, this will be send when the SRM is back online. |
| | 17 | * '''Martijn will''' contact the people in Utrecht for their genotype data, so we can continue with these analyses once the samples are uploaded. |
| | 18 | * '''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 |
| | 19 | |
| | 20 | == QC Issues == |
| | 21 | * Jeroen will look into the QC-metrics generated from the first 2300 samples. |
| | 22 | * Peter-Bram will look into pairwise correlations. |
| | 23 | * Lude asked if any cohorts have more details on the cell counts, Martijn will look into this. |
| | 24 | |
| | 25 | == Pipeline on the Grid == |
| | 26 | * 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. |
| | 27 | * 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) |
| | 28 | |
| | 29 | == Update on e/splice/trans/polyA-QTL analyses == |
| | 30 | * 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. |
| | 31 | * Peter-Bram talked with Renee about spliceQTLs, she will write some ideas down by the end of this week. |
| | 32 | * Peter-Bram obtained list of sites known to be troublesome in eQTL analysis |
| | 33 | |
| | 34 | == Any Other Business == |
| | 35 | |
| | 36 | * Maarten has joined the call today, he will be working mostly on Methylation data at the LUMC |
| | 37 | * On the RNA-course in Leiden last week, somebody from outside offered to help in this project, Lude will contact this person |
| | 38 | |
| | 39 | Next call is on Tuesday 12-11-2013 at 15:00. |
| | 40 | |
