Changes between Initial Version and Version 1 of 20131112


Ignore:
Timestamp:
Nov 12, 2013 3:00:33 PM (11 years ago)
Author:
Jeroen van Rooij
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • 20131112

    v1 v1  
     1Dasha: = 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 
     39Next call is on Tuesday 12-11-2013 at 15:00.
     40