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Fig. 2 | Genome Biology

Fig. 2

From: FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

Fig. 2

Detection of individual replication forks. a BrdU content estimation methods. b Scheme of sample preparation. c Exemplary BrdU content profiles (B/(B+T) ratio; B, BrdU, T, thymidine) along nanopore reads using CNN (pink) or TM (green). Shown are examples for rightward- (1, 2) and leftward-moving (3, 4) forks, initiation (5, 6) and termination (7, 8) events, and multi-replicon patterns (9–11). d Venn diagram of the overlap between the CNN- and TM-detected forks. e Spearman correlation coefficients between four RFD profiles of the whole genome at 1 kb smoothing obtained by the indicated methods. Top to bottom: FORK-seq TM and CNN, sequencing of EdU-labeled Okazaki fragments from MCM869 (OK-seq) and of accumulated Okazaki fragments from a ligase mutant [14]. f RFD profiles from the four different methods for chromosome V. Bottom, known origins from OriDB [23] (violet, late, cyan, early; color intensity reflects OriDB classification: bright, confirmed, medium, likely, light, dubious). Vertical dotted line, confirmed origins

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