# Occupancy of TFs with the target genes

The occupancy of SMARCD3 in the target genes listed below. I want to see average, normalized ChIP-seq signal at the promoter proximal region (1000bp upstream and downstream of the TSS).

I have 4 different experimental conditions (overlayed in one plot, per target gene using different color codes) where we want to visualize the changes in occupancy of GATA1 under all the conditions at individual gene promoters. The following are our target genes

1. ABCB1
2. ABCC1
3. ABCC2
4. SNAI2

So how GATA1 occupancy is changed across all these target genes across 4 different treatment condition.

So far what i have done

1. Aligned the samples
2. Done peak calling
3. Annotated the peak

I did steps 2 and 3 using homer.

Now after all this how do I find the occupancy of a TF with its target genes? Do I get the information from my peaks annotated output or from the peak files?

• For finding the nearest gene, just use bedtools nearest from bedtools. – Devon Ryan Jun 19 '19 at 20:42