After aligning and peak calling ATAC SEQ data, I used the homer getDifferentialPeaks script to do pairwise comparisons between samples.
This produces a file that contains the peaks enriched in sample1 vs. sample2.
Then I used findMotifsGenome.pl (also homer) on the differential peaks file to try to determine which transcription factors might be more active in sample1 compared to sample2.
I am having trouble interpreting the results, in part because the motifs that have been found are highly conserved, yet the transcription factors associated with those motifs are different.
As you can see in the image, the first ten hits all have something like: TGA[CG]TCA
But all are associated with different TFs, albeit with some similarity (Fos/Fosl2, Fra1/Fra2, JunB/Jun-API).
Any help making sense of these results, or suggestions for further/different analyses would be appreciated!