Genome scale DNA footprinting with DNase1, coupled with deep sequencing is a method called Digital Genomic Footprinting (DGF) that can give information about transcription factor occupancy in a single experiment. Transcription factors bound to DNA can impart unique “signature” in DNase1 DGF experiments. vChip uses these protein specific signature patterns at the known binding sites to train the machine learning “support vector machine” (SVM) models. These models are used to detect the instances of TF binding in the chromatin where ChIP-seq data is not available in the same or different cell lines. https://github.com/narekum/vChIP
vChIP
