Minutes RNA-Seq Analysis group (2014-04-22 15:00-16:00)
- Peter-Bram 't Hoen (LUMC)
- Maarten van Iterson (LUMC)
- Renée de Menezes (VUMC)
- Dasha Zhernakova (UMCG)
- Martijn Vermaat (LUMC)
- Leon Mei (LUMC)
- Patrick Deelen (UMCG)
- Michiel van Galen (LUMC)
- Lude Franke (UMCG)
- Jeroen van Rooij (EMC)
eQTL analysis
Dasha showed some results about the cis-eQTL genes compared by abundance of the gene, showing that most cis-regulated genes are in the higher expressed genes. Additionally, Dasha showed some results about comparing the eQTL mapping by TMM or CQN normalization methods, which were discussed during the call. We concluded to look a bit further into this by comparing to other datasets/papers like the GEUVADIS data and the RS/CODAM sample-sets.
Maarten
Working with Szymon on the Transcription Factors Binding Site analysis, this is also pending on the results of the normalization methods. We briefly discussed some ideas on the best approach on this.
Jeroen
About 600 samples from NTR were uploaded, samplesheet still te be send around.
Michiel
Continue-ing to work on the data management and grid/pipeline supporting.
Martijn Vermaat
Working on the Poly-A QTL analysis pipelines, troubleshooting some technical issues (zeros/missing data). Will also continue with the annotation databases to integrate to our analyses.
Patrick
Working on annotations of the eQTLs together with Maarten. Also looking at transQTLs through gene-network analysis, these 2 projects were briefly discussed during the call.
Renee
Working on spliceQTL analysis, already started and mostly scripted. Also working with Geuvadis data to develop additional statistical tests that might be applied to our data in time.
Dasha
Already discussed, but also continue on the meta-exon analysis. We also discussed looking at the exon-eQTLs.
Any other business
Face to face meeting on the 21st of May
