Extended Data Fig. 2: Estimation of T-to-C transition probability within nascent reads.
From: Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density
(a) As an example, the number of reads with one or two T-to-C transitions is shown for IN mRNA of the 40 min 4sU labeling timepoint of experiment 1 from RAW264.7 macrophages. (b) The number of reads with two or three T-to-C transitions is shown for the same sample as in (a). (c) Assuming a binomial distribution, the probability for a T in a read originating from nascent mRNA to transition to C is estimated separately from the ratio of reads containing two to one T-to-C transitions and from the ratio of reads containing three to two T-to-C transitions, for every population of reads based on the number of Ts in the reference. (d) T-to-C transition probability after subtracting a background probability that was estimated by minimizing the discrepancy between the two estimates shown in (c). (e) Estimated number of nascent reads among reads without T-to-C transitions. (f) Estimated number of nascent reads with more than three T-to-C transitions.
