An automated quality control pipeline for eQTL analysis with RNA-seq data

Expression quantitative trait loci (eQTL) analysis is of critical importance to understand the mechanism underlying trait associated variants. Evaluating and controlling the data quality of transcripts and genotypes, which are basis of eQTL analysis, remains challenging for researchers with limited computational backgrounds. There is a strong need for a user-friendly and comprehensive tool to pre-process those data sets automatically. Here we propose such a solution, eQTLQC, an automated quality control pipeline for preprocessing both RNA-seq and genotype data. The eQTLQC pipeline provides multiple informative quality control measurements and data normalization approaches. And it provides a easy-to-use configuration file for users to flexibly set up the parameters and control the pipeline. We demonstrate its utility by performing RNA-seq and genotype preprocessing on real data sets. eQTLQC is open source and freely available at https://github.com/ruanjunpeng/eQTLQC.