A question to get intuition

[MaryGoAround]

Hello

Indeed, this is not an issue with your software, rather my question please;

If I am not wrong, let's see, cell-ranger pipeline already runs macs2 and generate fragment file

Then, what is the point to peak calling by ArchR once again?

Sorry if my question seems stupid

I also after peak calling steps get this plot instead of gene name with chromosomes

[rcorces]

Please note that Issues are reserved for bug reports. questions about usage should be posted in Discussions as stated in the Issue template. I have converted this for you.

[rcorces]

cellranger-atac does not use MACS2 to create the fragments file. This is created directly from the bam file.

Your second question is not entirely clear but I would ask why you are expecting to get genes when you are plotting a heatmap of the peak matrix.