Extended Data Fig. 7: Comparison of PRAISE and the CMC-based Ψ methods, including Ψ-seq, Pseudo-seq, CeU-seq.

(a) Venn diagram depicting the overlap of Ψ sites detected in mRNA between PRAISE and Ψ-seq. (b) Deletion rates of Ψ-seq-only sites in PRAISE (n = 231) and random ‘U’ sites in PRAISE (n = 2,000). They had about 2% deletion rates and are higher than the background signal, but were not called because they are below our 5% cutoff. (c) Read coverage of Ψ-seq-only sites in PRAISE (n = 231) and PRAISE-only sites in Ψ-seq data (n = 2,101). (d) Venn diagram depicting the overlap of Ψ sites detected in mRNA between PRAISE and Pseudo-seq. (e) Venn diagram depicting the overlap between PRAISE and CeU-seq Ψ sites. (f) Pi chart of CeU-seq-only sites in PRAISE data. ‘Low coverage’ represents the coverage is lower than 20 reads. ‘High p value’ represents the p-value is higher than 0.0001 in PRAISE data. (g) Deletion rates of CeU-seq-only sites with sufficient reads in PRAISE (n = 776) and random U sites in PRAISE data (n = 2,000). (h) Pi chart of 1,642 PRAISE-only sites in CeU-seq data. (i) Stop rates of 48.2% of PRAISE-only sites with read coverage in CeU-seq data (n = 791). Data from three replicates are shown. (j, k) Venn diagram depicting the overlap between PRAISE sites and highest (j) or high (k) confidence sites from Safra et al in Genome research 2017. (l) Deletion rate of non-overlapped ‘high-confidence’ sites in PRAISE (n = 542) and random U sites in PRAISE data (n = 2,000). (m) Read coverage of non-overlapped ‘high-confidence’ sites in PRAISE data (n = 542) and PRAISE-only sites in Ψ-seq data (n = 1,758). Box plot middle lines mark the median and the boundaries of the box indicate the 25th and 75th percentiles; whiskers encompass all data that are not considered outliers.