A Dual Approach to Evaluate the Performance of RNA-Seq Data Analysis Pipelines with Weak Signals

Selecting the optimal pipeline is particularly challenging in complex scenarios with weak signals.This study highlights the significant impact of pipeline selection on RNA-Seq data analysis, particularly in contexts characterized by weak transcriptional signals, as in this study for low-dose metallic particle exposure.

By evaluating 90 bioinformatics pipelines using two complementary approaches — correlation with qRT-PCR data and classification performance — we were able to identify optimal configurations that ensure both analysis robustness for biological relevant observation.