Assign gene to peak in bulk ATAC-seq

Question

[Chris]

Hi all,

I have some questions about bulk ATAC-seq that I don't understand, hope that you can help. If we have a task to identify which genes in a sample (such as diseased) are in open chromatin region, is that using differential peaks give us better accuracy than using non-differential peaks? So we should have a normal sample and use tool such as Diffbind, Chipseeker to identify these genes? If I don't see a gene after annotation, could we say that gene is not in open chromatin region? Is using findMotifsGenome.pl in Homer with the input differential peaks can give us which transcription factors cause the diseased? Would you please tell me which package we can use to make this plot?

I try to do a similar analysis as this paper:
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09349-7

Thank you so much for your help!