Novel examples of NMD escape through alternative intronic polyadenylation

Custom scripts, Jupyter notebooks and processed data generated during the analyses for manuscript "Novel examples of NMD escape through alternative intronic polyadenylation". The presented notebooks document the analysis workflow of the manuscript. In short, candidate-event lists are generated first, then GTEx tissue-level junction support and surrounding-exon coverage are summarized, then these summarized data are used to filter candidate events, generate figures and final output tables. Contents: R notebooks used to generate lists of candidate events - poison exons followed by a PAS (ATE-PE_from_PAS(IorII).ipynb for cases I and II, ATE-PE_from_novel_junc(III).ipynb for case III) Bash scripts that collect preprocessed GTEx coverage and junction data (scripts in ATEPE_from_PAS_data/ and ATEPE_from_novel_junc_data/ folders) R notebooks that summarize GTEx tissue-level junction support and coverage (tissue_data_PAS(IorII).ipynb and tissue_data_novel_junc(III).ipynb) R notebook that assembles manuscript diagrams and figure panels from summarized data: diagrams_fig2,3,4.ipynb Data table with 50 events that undergo tissue-specific isoform switch: tissue_specific_hits.allcases.dtau025_qval01.n50.csv (raw table for manuscript Table 1) Supplementary Data File 1 - 451 candidate events of NMD escape via intronic polyadenylation (DataTable1.csv) Columns include gene name, poison exon coordinates, exclusion junction coordinates, case (I, II or III), stop codon coordinates; metrics calculated from GTEx data: tau range, min(tau), psi1 range, cor(psi1, tau), p-value of the correlation test, adjusted p-value (qval); PAS coordinates and PAS source - TE (annotated), pAread or PolyASite; for case I and II: pAread support and PAS usage in polyASite; for case III: total split read support of I2 junction in GTEx. .RData files generated by the notebooks, including intermediate GTEx-derived data and preprocessed NMD inhibition data. README.md with a detailed description of the archive contents, short analysis workflow and required packages.