I have two RNAseq data, including case and control. I want to analyze alternative polyadenylation between those groups. I find that there are several programs doing that. my question is how to detect alterations of APA with Fisher's exact test.
1 answer
You can't analyse differences in APA with any common statistical test that I know of.
Instead use one of the pieces of software designed to do this analysis. All of them will output p-values or q-values, and some sort or measure of effect size. As well as the qapa mentioned by @Amar, we have successfully used Dapars (https://github.com/ZhengXia/dapars). There are also many others such as TAPAS (https://academic.oup.com/bioinformatics/article/34/15/2521/4904269).
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Why not use these programs? Their statistical analysis is more robust than a simple Fisher's exact test. Here's one with decent documentation: https://github.com/morrislab/qapa
oh. thanks. I just want to know which one statistic method, such as Fisher's exact test, can analyze the statistic differences for APA.