Despite its powerful applications, DNase-seq has some limitations:
Complexity of Data Analysis: Analyzing DNase-seq data requires sophisticated bioinformatics tools and expertise. Resolution Limitations: While DNase-seq can identify accessible regions, it may not always pinpoint the exact binding sites of transcription factors. Sample Quality: The quality of the starting material, such as tissue samples, can significantly affect the results. Enzyme Bias: DNase I digestion may have sequence preferences, which could introduce biases in the detection of hypersensitive sites.
