Hello,
I have ATAC-seq data (control and treatment), i am interested in calling enhancers and super-enhancer using this data. While i have executed ROSE algorithm from young`s lab on his dataset from chiq-seq. I am wondering if i can use ROSE on ATAC-SEQ and how can i confirm that the output from ROSE On ATAC-seq are SE/TE and not promoters??
Sure, you can run it on them. Stitching tends to happen less frequently since the ATAC peaks are generally less wide than H3K27ac, but it'll run fine.
ROSE excludes peaks within 2.5kb (I think) of the TSS from its stitching process. So while the resulting SEs may overlap promoters, there is some effort to avoid calling SEs that are driven pretty much solely by a promoter. ROSE also has some hidden logic/behavior where stitching will not occur if the stitched region spans the TSS of 3 or more genes. This causes gene-dense regions that look to have clear super enhancers by eye to be missed.
The annotations are also at least a decade old, and you have to alter the source code to provide new ones. Which I've found to be worth doing.
It's software that could really use some updates at this point, frankly.
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