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 technique to ChIP-seq and CUT&Run for detecting enrichment of protein-DNA interactions or histone modifications. A detailed description of the ​experimental method together with a ​protocol for computational analysis have been published by the Henikoff laboratory. Our preferences for specific steps include:

• As in the analysis protocol from the Henikoff lab, we recommend using an IgG control.
• As an alternative to calling peaks with ​SEACR, we recommend using ​MAC2 because the resulting peaks tend to be narrower and better capture the tagged regions.

   macs2 callpeak --keep-dup all -t sample.mapped.bam -g hs -f BAMPE -n OutputName
  

• 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 in the ​analysis protocol published by the Henikoff lab, is useful for visualization of the CUT&Tag profile with a genome browser.
• Spike-in normalized bedgraph files are not an appropriate input for MACS2, since MACS2 will renormalize to the library size.

For a working example for how to run the published analysis workflow using the computing resources at the Whitehead Institute, please follow /nfs/BaRC_Public/BaRC_code/pipelines/analyze_CUTnTag/README and find the associated scripts within the parent directory.