I am working with ATACseq data and pursuant to calling peaks I am interested in identifying transcription factor binding sites using the called peaks. Has anyone had success using TFBS tools, MotifBreakR, or Diffbind to identify transcription factor binding sites and any SNP located in these areas? Are you using any different tools to investigate peaks? I am new here so I appreciate your thoughts
Personally I use MEME and TOMTOM for calling enriched sequence motifs and intersecting them with known transcription factor binding sites.
Taking your peaks of interest you can convert them into BED format, then use
bedtools getfasta to convert them into FASTA format. Running MEME will identify any enriched sequence motifs (it's a nice unbiased method that identifies ANY enriched sequence). Then taking the MEME output you can run TOMTOM to see if any of the sequences that are enriched in your peaks overlap with known transcription factor binding sites.
I've seen this paper and tool yesterday. Hope they can help.