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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.
