CUT&Tag

Cleavage Under Targets & Tagmentation (CUT&Tag) is a tethering method that uses a protein-A-Tn5 (pA-Tn5) transposome fusion protein. It is an alternative to ChIP-seq and CUT &Run. This ​page contains a detailed description of the method. This ​page describes the computational analysis proposed by the Henikoff laboratory. These are our preferences for specific steps:

• Like the Henikoff lab analysis method, we recommend using an IgG control.
• We recommend using ​MAC2 to call peaks because the peaks tend to be narrower and better capture the tagged regions.
• We recommend not removing duplicates from any of the samples.
• Spike-in calibration using the number of fragments mapped to the E. coli genome, as described on the Henikoff lab analysis, is be useful for visualization of the CUTTag profile on a genome browser.
• Spike-in normalized bedgraph files are not an appropriate input for MACS2, since MACS2 will renormalize to the library size.