I have questions about performing repeat-elements (RE) analysis in ATAC-Seq data.
So, I have RE information from repeatmasker
Now, I have
bam files from ATAC-Seq.
I think I have 2 approaches to know which repeat-elements have less or more chromatin accessibility (depending on how I want to look at the RE):
- Read the counts in the windows of each RE transcript and perform differential analysis.
- Read the counts at the sub-family level and perform differential analysis.
Is my approach correct, statistically?