[Inquiry] How to generate blacklist for bat genome?

[GarlicPaasta]

I am interested to perform ATAC seq on bats. As part of the standard pipeline for ATAC seq processing, a blacklist is traditionally used to omit repititive reads, however, this resource is not available for bat.

I have a few questions:

1. In studies that perform ATACseq on non-model organisms, rarely a blacklist is used. In this regard, is the analysis flawed?

2. I wanted to generate a blacklist for the bat species I am working with - Eonycteris spelaea. I am unsure of the input files needed for this. May I enquire what is the file needed for (a) input and (b) mappability files? (as well as how to generate these files?)

   • Blacklist execuatable
   a. input/ - folder containing all bam and bam.bai files
   b. mappability/ - folder containing all uint8 Umap files

Thank you for your kind assistance in this matter!