Differential_polyadenylation

Contents: nanopolish: direct RNA datasets analysed by nanopolish - raw_data: merged data between nanopolish and npTranscript results - analysis: testing changes in poly(A) length between control and infected using Wilcoxon's test of ranks with log-transformed data of Calu-3 48hpi direct RNA dataset - scripts: example scripts for testing changes in poly(A) length between control and infected using Wilcoxon's test of ranks, and also with log-transformed data tailfindr: direct cDNA datasets analysed by tailfindr - scripts: example scripts for poly(A) vs poly(T) correlation, mixed_model and generating raincloud plots for poly(A) length - raw_data: merged data between tailfindr and npTranscript results - analysis: tailfindr outputs and mixed model analysis outputs where files with names ending with 'int' shows the coefficient (changes in log tail length relative to control (intercept), and files with names ending with 'log_nofilter' shows the padj values for changes between control and infected poly(A) lengths. nanopolish_vs_tailfindr: - raw_data: median poly(A/T) lengths from nanopolish and tailfindr (before log transformation) - analysis: Spearman's correlation tests between nanopolish poly(A) and tailfindr poly(A/T) median lengths - scripts: example scripts for generating Spearman's correlation tests between nanopolish poly(A) and tailfindr poly(A/T) median lengths tailfindr_scripts: -tailfindr-related scripts only tailfindr_calu_48hpi_analysis: - analysis results files from calu 48 hpi dataset including 'meancalc' - working sheet for backtransforming and calculating difference in log-tranformed poly(A) lengths between control and infected - control: intercepts for control - infected: coefficients for infected - mt: mitochondrial genes - nonmt: non-mitochondrial genes