idcheck

In modern biology research, a growing subdiscipline of genomics is seeking to integrate large-scale and diverse biology feature data sets in order to achieve a more complete comprehension of a biological process. When analyzing data obtained on the same individuals with different assays, sample assignments must be rigorously controlled as any sample confusion may lead to erroneous deductions about the relationships between different biological measurements. Expression quantitative trait loci (eQTLs) integrate genotype data and gene expression data to investigate how genomic loci regulate expression levels of mRNAs or proteins. Before the analysis begins, however, it is important to check sample consistency, i.e. determine if genotype and gene expression data putatively from the same samples are correctly assigned. In this application note, we introduce a tool (IdCheck) that allows easy assessment of genotype (SNP arrays) and gene expression (RNA sequencing, RNA-seq) sample identity checking. IdCheck compares the identity of RNA nucleotide and genotype, and then it calculates a match ratio. Based on this ratio, we can determine how the samples are paired. Our tool provides a fast and efficient way to evaluate the potential sample mix problems for any number of genotype array and RNA-seq lane pairs.