Geuvadis RNAseq Teleconference April 26, 2012 Minutes
Written by Tuuli L.
- Tuuli gave an update on the data
o mRNA
§ Fastqs are all OK, and there’s a freeze folder on the ftp site. Natalja should change the write access so that only her and Tuuli can modify the content of that folder.
§ There are no sample swaps in the data, but 5 samples show increased heterozygosity in RNAseq data suggesting some cross-contamination. These samples are included in the fastq freeze but will be excluded from the analysis. Tuuli has flagged them in all possible READMEs.
§ The data has been mapped both with bwa and GEM. The latter gives better results, and if the GEM manuscript is submitted very soon, it will be the mapper to use in this project. Tuuli’s analysis for the CSHL poster is based on bwa due to time constraints.
§ Data quality seems excellent: lab effects are not a major problem
o miRNA
§ Sequencing data of the last 48 samples from Kiel are still missing, but the fastqs will be uploaded probably within 2 weeks but certainly by the end of May
§ Marc F. has been running this pipeline for miRNA QC and quantification, results to expect very soon
o Genotypes
§ Imputation of the ~40 1000g Phase2 samples has some issues. This has to be sorted out soon.
- Discussion on whether we should aim to publish a separate QC paper before the main paper. The consensus was not to do this.
- The analysis group meeting in Geneva in April 16-17 was very productive and people enjoyed it. The next meeting will be in Barcelona in the end of June or early July; everyone involved in analysis is welcome to attend.
- Tuuli presented the analysis plan that was put together by the analysis group in Geneva. Some minor additions.
- Discussion about collaborations with members of the 1000g analysis group: Kai Ye (Leiden) from the structural variation group would like to look into effects of CNVs, and we’ll discuss with him in more detail how he’d contribute. Daniel McArthur (Boston) from the functional interpretation group will be involved in loss-of-function analysis.
- Deadline for any analysis for the CSHL poster is May 1st, but anyone planning to contribute should let Tuuli know in advance
Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen@unige.ch