iam new to this field i come from computer science, i have taken many peak files from the ENCODE chip-seq experiment matrix and annotated them .I chose the promoters , upstream of each gene within distance(5000,1000) in the file and now I have a file with gene names and entrez_ids. I wonder every line of this file is a binding site of the specific TF ?
Every line of a peak file is supposed to be a binding event of that protein (or whatever the molecule which was targeted by antibody). The main problem with the chip-seq peak is, chip seq technology is not very precise as the specificity of the binding even. So you can say that specific protein is bound to that interval but i wouldn't be so sure about the specific location. ( you need validation) or you can also check chip-exo (which is very similar to chipseq that also higher specificity.)
Like in the any experiment in the science, there is also a chance of false positives. You might also need to keep in your mind.
In general in a file of ChIPseq peaks each line represents a region in which the signal is enriched in the ChIPped sample with respect to the input sample (making the general assumption that the experiment included input samples and that peaks were called taking advantage of this).
It's not correct to say that each peak is a transcription factor binding site. Even if you had 100% specificity you could imagine that each peak contains a TFBS, but there will be part of the peak that is not part of the binding site (a typical TFBS much shorter than the typical ChIPseq peak; see also this post here for some more insight: https://www.biostars.org/p/163205/). Besides this, most likely a portion of the peaks will be a-specific, even if you filtered on FDR and used the input to assess enrichment.
Please note that if you don't give further information the average reader will have no clear idea about the functions you mention (annPeaks and addGeneIds: they are functions of a package? A software? A suite?). Improving the detail of your question will improve the specificity of the answer.
Thanks for your reply @morovatunc and @Satya and but i cant knock down a protein my validation should be strictly programmatically i am not in a real lab. I created an app in R that finalyafter annotating the peaks and filtering , it takes the promoters near TSS of files i download programmatically from ENCODE CHip-seq Experiment matrix , i need a validation for what iam doing but dont know what that would be...