infer NFRs from H3K27Ac ChIP-Seq data?

Question

[ZUCM]

Hi there,

I am trying to do motif analysis on H3K27Ac peaks and I think that taking the whole peak region as input to scan TFBS is bulky and inaccurate. So I used Homer findpeak script to find the nucleosome-free regions but it did not provide ideal results as only one NFR will be identified per peak. Are there other tools that can infer putative NFRs from enhancer data better than homer?

Thanks!

[ATpoint]

I guess it depends a bit on the fragment length the the chromatin was sonicated to but in an ideal worls you will not pick up the NFR by H3K27ac as you get the position of the histone and this is then of course not the NFR but the flanking regions. Scanning the peak itself is probably not informative as the TF binding happens as you say in the NFR. Maybe take the peaks and choose a, say 500bp flanking regions and scan that. If you have ATAC-seq data from the same cell type you could use the center of overlapping ATAC-seq data which approximates the NFR pretty well.