I am interested in the differential expression of splice junctions. For this purpose I have a count matrix containing counts (per sample) from reads spanning each splice junction. I want to perform a DE analysis on the splice junction level and I have not found any suitable tools for this task.
I am aware of one method:
but I am reluctant to use it, because DEXSeq is too computationally expensive for the number of samples I have.
I have already used a voom-limma pipeline for DE analysis of genes & transcripts, as well as a voom-diffSplice pipeline for DE analysis of exons.
- Now I am curious if a voom pipeline would be suitable for DE of splice junctions (I remember having read somewhere, that limma is suitable for any genomic feature, but since a splice junction consists of 2 borders and does not have actual length, I am wondering if it would be a valid analysis.)
- If it is, then I'm unsure if voom-limma or voom-diffSplice is more appropriate for this purpose
I would appreciate any help or caveats regarding such an analysis with limma, or any tip regarding the use of other tools to perform such an analysis.
Thanks in advance!