Soumyashant Nayak

BEERS2 simulates RNA-seq reads with high fidelity, incorporating detailed library preparation and sequencing steps, and evaluates its impact on the Salmon pseudoalignment algorithm.

This study evaluates isoform quantification methods using simulated data, finding that no method significantly outperforms a simple approach on realistic data.

The paper introduces a framework to rank genomic features by differential effect size, showing that pseudocounts optimize the balance between fold-change and difference sorting.