I have a question about fold change and how it should be calculated for enhancer regions. I am aware that packages such as DESeq2 and edgeR will calculate the fold change for genes, but I am interested in calculating fold change at enhancers.
I am quite naive and new to RNA-seq data, and it's possible that something like this is not entirely feasible, but i'd rather ask the experts.
So my questions can be summed up as the following:
Is it possible to calculate the fold change of 'expression' at enhancer regions? Is this something that can be feasibly done with RNA-seq data?
Is the information in this thread still relevant and if so could I implement this idea of log2 coverage / read counts at enhancer regions to compare against enhancer associated promoter fold change?
I am trying to use this information to answer whether there is any correlation between eRNA expression at enhancers and gene expression at promoters. One thought is that if I have high eRNA expression, I would see high gene expression in the 'associated' gene.
I appreciate all the help! I'm looking to learn, so any information regarding anything in this post is appropriate.