Quantification of acetylation enriched regions at transcription factor binding sites (WT vs KO)

Question

[massimofaggiani]

I am still at the beginning of ChIP-seq data analysis and am stuck in the following problem: I want to quantify the enriched peaks of H3K27ac at the proximity (5kb) of each binding site of a transcription factor under study, and make a comparison with the knock-out of the same TF. I have already calculated the total number of H3K27ac peaks that fall in the 5kb range between the 2 conditions but not for each binding site. How could I accomplish this, given also the total number of TF binding sites? And then, how could I represent it graphically? Thank you.

Answer 1

[Prakash]

One suggestion would be to quantify the H3K27ac enrichment ± 5kb (or ± 2kb) relative to peak summit for the given set of identified TF binding sites of your interest. This can be performed in HOMER using option e.g -size 5000 -hist 10 . More detail can be found here . Further graphically it can be represented in R using basic plot function or ggplot2

[massimofaggiani]

Thank you for your answer, but I managed to do that simply by adding -c (count) option in bedtools window command. Now I would like to filter only the regions for which there is an increase in acetylation peaks in the TF knock-out with respect to wild-type, having two separate bed files. Any suggestions?