I am trying to identify the target genes of my transcription factor after ChIP-seq. I have called the peaks and I have also looked at the number of reads falling around the Transcription Start Site of each gene. I am wondering how to define if a gene is bound by my TF.
Does it make sense to do the following: Pick a cutoff value for number reads (per million) falling into (for example) +-2kb of the TSS. I've made heatmaps so I could estimate by eye the number of genes bound, and take the cutoff value from this, but this seems a bad idea. I also don't want to simply assign a peak to it's nearest gene and, provided it's close to the TSS, call the gene a target, that seems much too liberal. Similarly, looking at my heatmaps and picking e.g. 'the top 200 genes' also seems flimsy.
Is there a robust definition for whether a gene is a target or not, using ChIP-seq data?
Any advice would be most apreciated.