Inquiry Regarding Absence of Blacklist Regions for Sus scrofa in ATAC-seq Analysis

[tianxuekai]

I hope this message finds you well.

I am currently using your excellent package [Signac ] for single-cell ATAC-seq analysis in pig (Sus scrofa, genome: Sscrofa11.1). I noticed that, unlike human or mouse, there is currently no publicly available blacklist BED file for this species.

As blacklist regions are often recommended for quality control (e.g., computing FractionCountsInRegion() or filtering noisy peaks), I would like to ask:

What would you recommend in cases where official blacklist files are not available?

Is it reasonable to skip this step entirely, relying instead on TSS enrichment and nucleosome signal for cell-level QC?

Alternatively, would you advise generating a custom blacklist (e.g., based on high fragment count bins)? If so, are there any best practices or tools you would suggest?

Your insights would be greatly appreciated, and I thank you for your continued support of the community through your outstanding work.

Best regard