== 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 [https://yezhengstat.github.io/CUTTag_tutorial/index.html experimental method] together with a
[https://yezhengstat.github.io/CUTTag_tutorial/ 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 [https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-019-0287-4 SEACR], we recommend using [https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html 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 [https://yezhengstat.github.io/CUTTag_tutorial/ 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.