wiki:20131112

Version 1 (modified by Jeroen van Rooij, 11 years ago) (diff)

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Dasha: = 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.