Changes between Version 15 and Version 16 of SOPs/CUT&Tag


Ignore:
Timestamp:
08/02/24 11:43:31 (7 months ago)
Author:
ibarrasa
Comment:

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  • SOPs/CUT&Tag

    v15 v16  
    1212  * 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.
    1313  * Spike-in normalized bedgraph files are not an appropriate input for MACS2, since MACS2 will renormalize to the library size.
    14 
     14  * Spike-in normalization using the commands described in [https://github.com/macs3-project/MACS/wiki/Advanced:-Call-peaks-using-MACS2-subcommands/ Call peaks using MACS2 subcommands, step 4 ] hasn't worked well for us.
     15  * We recommend using the spike-in scale factors in subsequent steps when comparing binding between conditions using tools like DESeq2.
    1516For 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.
    1617