Minutes RNA-Seq Analysis group (2013-11-05 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)
• Patrick Deelen (UMCG)
• Freerk van Dijk (UMCG)
• Dasha Zhernakova (UMCG)
• Rick Jansen (VUMC)

Data Generation and Upload

• SRM was down last week, 240 samples are ready to send in Rotterdam, this will be send when the SRM is back online.
• Martijn will contact the people in Utrecht for their genotype data, so we can continue with these analyses once the samples are uploaded.
• 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

QC Issues

• Jeroen will look into the QC-metrics generated from the first 2300 samples.
• Peter-Bram will look into pairwise correlations.
• Lude asked if any cohorts have more details on the cell counts, Martijn will look into this.

Pipeline on the Grid

• 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.
• 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)

Update on e/splice/trans/polyA-QTL analyses

• 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.
• Peter-Bram talked with Renee about spliceQTLs, she will write some ideas down by the end of this week.
• Peter-Bram obtained list of sites known to be troublesome in eQTL analysis

Any Other Business

• Maarten has joined the call today, he will be working mostly on Methylation data at the LUMC
• On the RNA-course in Leiden last week, somebody from outside offered to help in this project, Lude will contact this person

Next call is on Tuesday 12-11-2013 at 15:00.