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.
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).
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
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.