iSeqQC: A Tool for Expression-Based Quality Control in RNA Sequencing

ABSTRACT Quality Control in any high-throughput sequencing technology is a critical step, which if overlooked can compromise the data. A number of methods exist to identify biases during sequencing or alignment, yet not many tools exist to interpret biases due to outliers or batch effects. Hence, we developed iSeqQC, an expression-based QC tool that detects outliers either produced by batch effects due to laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers. It can be utilized either through command-line (Github: https://github.com/gkumar09/iSeqQC ) or web-interface ( http://cancerwebpa.jefferson.edu/iSeqQC ). iSeqQC is a fast, light-weight, expression-based QC tool that detects outliers by implementing various statistical approaches.