Changes between Version 3 and Version 4 of SOPs/CUT&Tag


Ignore:
Timestamp:
04/02/24 14:39:49 (10 months ago)
Author:
twhitfie
Comment:

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  • SOPs/CUT&Tag

    v3 v4  
    11== 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.
     2Cleavage 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.
     3A detailed description of the [https://yezhengstat.github.io/CUTTag_tutorial/index.html experimental method] together with a
     4[https://yezhengstat.github.io/CUTTag_tutorial/ protocol for computational analysis] have been published by the Henikoff laboratory. Our preferences for specific steps include:
     5  * As in the analysis protocol from the Henikoff lab, we recommend using an IgG control.
     6  * 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.
    77{{{
    88 macs2 callpeak --keep-dup all -t sample.mapped.bam -g hs -f BAMPE -n OutputName
    … …  
    1010
    1111  * We recommend not removing duplicates from any of the samples.
    12   * 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.
     12  * 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 be useful for visualization of the CUTTag profile on a genome browser.
    1313  * Spike-in normalized bedgraph files are not an appropriate input for MACS2, since MACS2 will renormalize to the library size.
     14
     15For 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.