I have microRNA-seq count data from several experimental conditions. Most microRNA transcripts produce two forms of mature (bioactive) microRNAs (the 5p arm and the 3p arm). In my RNA-seq read data, reads align to either of the mature forms (which are disjoint locations in the microRNA transcript), or to other regions in the transcript not compatible with either mature forms.Hence, for each microRNA transcript I have 3 categories. (I can actually define more categories since reads that are compatible with the mature forms often include modifications),
What I want to test is whether the proportions among the 3 categories mentioned above are affected by my experimental conditions (i.e., factors). Is there anything in limma, or other RNA-seq count based packages, that can be used for this question?
I think that a GLM with a Dirichlet multinomial distribution, as implemented in the MGLM package, might be relevant but haven't used it and would assume that is not doing as good of a job in modeling the variance like voom.
Thanks a lot,