I have ATACseq data for two yeast species. I have called peaks with MACS2 and did occupancy and affinity analysis of peaks with DiffBind. Now I need to find motifs of TF binding sites in the peaks and compare those motifs between two species.
There is a ton of softs and databases for doing the task, so I am a bit confused on how to start with the analysis. Can anybody share the experience with motif search and motif comparisons, specifically which tools are considered as "best practices" in the field?