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.