Hi,
I've been reading about the way macs2 works on the cellranger fragments files, and begin to think that the current default settings might miss half of the useful signals.
From my understanding, both ends of the fragments from the cellranger output are cut sites and worth being included for peak calling. But currently, every fragment only shows up once in the fragments file. And when that is used as input for macs2, it will be taken like reads/tags, with only 5' end of each fragment being considered for shifting and extensions.
If what I described above is correct, then I would propose to add a function to duplicate the fragments and label the original fragments as on positive-strand while the duplicates on negative-strand prior macs2 peak calling. In this way, both ends of the same fragment can be included for peak calling.
Please correct me if I misunderstood how Signac handles macs2 peak calling, thanks!
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