I post today after long time without finding the proper answer to my question.
More or less the workflow for analyzing TF ChIPseq data is becoming clear:
ChIP --> Library preparation --> Sequencing --> Pre-filtering and QC check --> Mapping to reference genome --> Find enrichment signals (peaks) --> Motif Discovery to cross validate if the top ranked peaks present the TF motif
But I'm interested into rank all my peaks into some sort of indicator whether they have a presence or not of the desired TF and subset the peak list to the TF real ones. I have been trying with MEME/MEME-chip/TOMTOM/MAST and also with HOMER, but I'm getting confused because with these suites I'm not particularly sure I could obtain what I want (or maybe I missunderstood something)
So, my question is: Is there any way to rank the peaks according to the presence or not of the TF, just to add it to the peak calling statistics?
Thanks for your help and suggestions!