Hello,
I've done basic QC for miRNA samples. Attached is a sample sheet that
denotes samples to use in analysis. From the total 492 samples, 480
samples from 452 unique individuals pass QC. We end up having 705 genes
quantified in at least 50% of the samples - most of these have low
quantifications though.
Analysis of sample correlation and clustering shows even a clearer
population clustering than mRNA, and very little lab effects.
I've updated the QC section of the wiki with miRNA results: list of
samples to exclude, basic read count and mapping stats, and early
correlation analysis.
The data is on the ftp site:
- sample sheet: /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/qc
- quantifications:
/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/mirna/quantification_tables
I'm now running PEER normalization for miRNAs, and that data will
probably be the best to use for mRNA-miRNA correlations and eQTL
analysis. I'll let you know when this is done.
cheers,
Tuuli
--
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(a)unige.ch
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