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Fig. 7 | BMC Bioinformatics

Fig. 7

From: QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model

Fig. 7

Creation of the mock dataset with sample swop. A “mock” dataset can be created from the original dataset by swop half of the samples between the two experimental conditions. The differential RNA methylation result generated from the original data with correct sample label reflects biological meaningful difference; while the result generated from the “mock” dataset has no biological meaning. In theory, a good algorithm should pick up as many as differential methylation sites from the “genuine” dataset but as less as differential methylation sites from the “mock” dataset. The example above shows how a pair of “genuine” and “mock” datasets is created from two biological replicates - sample 1 and sample 2. Since the tested MeRIP-Seq dataset has 3 biological replicates under each condition, it is possible to create 3 pairs of “genuine” and “mock” datasets from 3 pairs of replicates, i.e., sample 1 and 2, sample 2 and 3, sample 3 and 1. It is then possible to compare the performance of different algorithms

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