| | 1 | == CUT&Tag == |
| | 2 | 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. |
| | 3 | This [https://yezhengstat.github.io/CUTTag_tutorial/index.html page] contains a detailed description of the method. |
| | 4 | This [https://yezhengstat.github.io/CUTTag_tutorial/ page] describes the computational analysis proposed by the Henikoff laboratory. These are our preferences for specific steps: |
| | 5 | * Like the Henikoff lab analysis method, we recommend using an IgG control. |
| | 6 | * We recommend using [https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html MAC2] to call peaks because the peaks tend to be narrower and better capture the tagged regions. |
| | 7 | * We recommend not removing duplicates from any of the samples. |
| | 8 | * 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 browser. |
| | 9 | * Spike-in normalized bedgraph files are not an appropriate input for MACS2, since MACS2 will renormalize to the library size. |
