We try to analyze scATAC-seq data; DiffBind is a good choice (probably the best one!) to identify differential peaks. The sequencing libraries are generated from brains of mice randomized in two groups treated with a compound and vehicle. 10x cellranger-atac is used for the initial read count and the output directories contain sorted bam files, but also bed files, notably, “peaks.bed”.

I am wondering if we could use those bed files as an input for DiffBind, instead of running MACS3/hmmratac (which is a great tool, as well), with all the preliminary and following conversions?

Your help is highly appreciated