Giacomo Baruzzo

Abstract Human cellular reprogramming to induced pluripotency is still an inefficient process, which has hindered studying the role of critical intermediate stages. Here we take advantage of high efficiency reprogramming in microfluidics and temporal multi-omics to identify and resolve distinct sub-populations and their interactions.

Precision-recall trade-off. Fig 6 shows the AUPR obtained by the methods in all configurations by averaging the values over the 50 simulations. The value of the area increases as the sample size increase, especially between SS = 10 and SS = 25. Instead, the percentage of DA features affects the AUPR more markedly at low sample sizes. Fig 6.

Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters.