Differential_polyadenylation

Contents: <br> 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<br> - 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<br> <br> <br> 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<br> - raw_data: merged data between tailfindr and npTranscript results<br> - 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.<br> <br> <br> nanopolish_vs_tailfindr:<br> - 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<br> - scripts: example scripts for generating Spearman's correlation tests between nanopolish poly(A) and tailfindr poly(A/T) median lengths <br> <br>

数据集内容：
nanopolish相关数据集：经nanopolish分析的直接RNA数据集，下设：
- 原始数据：nanopolish与npTranscript分析结果的合并数据集；
- 分析内容：针对Calu-3细胞感染后48小时（48hpi）的直接RNA数据集，采用对数转换后的数据开展Wilcoxon秩和检验（Wilcoxon's test of ranks），对比对照组与感染组的poly(A)尾（poly(A)）长度变化；
- 脚本示例：用于通过Wilcoxon秩和检验（含对数转换数据）对比对照组与感染组poly(A)尾长度变化的示例脚本。

tailfindr相关数据集：经tailfindr分析的直接cDNA数据集，下设：
- 脚本示例：用于poly(A)尾与poly(T)尾相关性分析、混合模型（mixed model）构建以及poly(A)尾长度雨云图（raincloud plots）绘制的示例脚本；
- 原始数据：tailfindr与npTranscript分析结果的合并数据集；
- 分析内容：包含tailfindr输出结果与混合模型分析结果，其中文件名以'int'结尾的文件为相对于对照组的对数尾长变化（截距项）系数，文件名以'log_nofilter'结尾的文件为对照组与感染组poly(A)尾长度变化的校正后P值（padj）。

nanopolish与tailfindr对比数据集：
- 原始数据：nanopolish与tailfindr输出的未进行对数转换的中位数poly(A/T)尾长度；
- 分析内容：针对nanopolish的poly(A)尾中位数长度与tailfindr的poly(A/T)尾中位数长度开展Spearman相关检验（Spearman's correlation tests）；
- 脚本示例：用于生成上述两组数据间Spearman相关检验的示例脚本。