I have an ATAC-seq dataset of three conditions, each with three replicas. After running MACs2 within a custom pipeline, peak files (narrow, summit and size filtered) for individual replicas and merged ones were obtained. Now, I would like to get peaks info (.bed and .fasta files) associated with specific genes. The aim is to use those peaks to do motif discovery and enrichment and correlate transcription factors with genes of interest. For that, I will use the MEME suite, in particular CentriMo, and will try Homer also. My question is: how to get the .bed and .fasta file of accessible peaks associated with such genes?
Any advice on downstream motif analysis would be greatly appreciated.
Thanks a lot in advance!