I have ATACseq data analyzed for my cell of interest. I also have RNAseq from my cells with/without stimulus. After doing differential gene expression from the RNAseq, I want to do motif enrichment in the promoters of this gene set (~4,000 genes). Specifically, I would like to use bedtools to intersect the DNA accessibility regions of the promoters of this gene set, to identify the regions with the highest likelihood of transcription factor binding.
Since RNA is stranded (can be on + or - strand) and ATAC is not, will there be any issue with using a standard bedtools command as follows?
bedtools intersect -a RNAseq_DEG_promoters.bed -b ATAC.bed > result.bed
Any help appreciated