Fig. 3

Performance of the DNAscent v2 forkSense subprogram. (a-b) Individual reads mapping to S. cerevisiae chromosome I are shown for S. cerevisiae cells (a) synchronised in G1 and released into BrdU and (b) asynchronous and pulsed with BrdU and chased with thymidine. Origins that are confirmed and likely from OriDB are shown in the top track. Eight reads are shown for each experiment where each read is represented as a group of three tracks: the probability of BrdU at each thymidine (upper track; from DNAscent detect) and the probability that a leftward-moving fork (middle track; from DNAscent forkSense) and rightward-moving fork (lower track; from DNAscent forkSense) passed through each position during the BrdU pulse. The y-axis of each track ranges from 0 to 1. (c-d) Pileup of all replication origins and termination sites called by forkSense that mapped to S. cerevisiae chromosome II for S. cerevisiae cells (c) synchronised in G1 and released into BrdU (2,980 origin calls from a total of 9,864 reads) and (d) asynchronous and pulsed with BrdU and chased with thymidine (1,461 origin calls from a total of 5,186 reads). Only reads with mapping length ≥20 kb and mapping quality ≥20 were used. The OriDB track shows confirmed and likely origins. For clarity, only the first 400 kb of chromosome II are shown; the full length of chromosome II is shown in Figure S5 in Additional file 1. (e) Distribution of the distance between each origin call and the nearest confirmed or likely origin from OriDB for S. cerevisiae cells synchronised in G1 and released into BrdU. The results of three versions of DNAscent are shown. RepNano only made a total of 14 origin calls on this dataset when run with the default settings, so these were omitted for clarity. (f) A similar analysis to Fig. 3e, but for asynchronous S. cerevisiae cells pulsed with BrdU and chased with thymidine. Results for DNAscent v2 are shown alongside results from the RepNano transition matrix (TM) and convolutional neural network (CNN) origin calling algorithms run using the default parameters. Earlier versions of DNAscent were not designed to call origins in asynchronous cells, so only the results from DNAscent v2 are shown