Changes between Version 2 and Version 3 of SOPs/CUT&Tag


Ignore:
Timestamp:
12/06/23 11:11:55 (17 months ago)
Author:
ibarrasa
Comment:

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  • SOPs/CUT&Tag

    v2 v3  
    55  * Like the Henikoff lab analysis method, we recommend using an IgG control.
    66  * 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{{{
     8 macs2 callpeak --keep-dup all -t sample.mapped.bam -g hs -f BAMPE -n OutputName
     9}}}
     10
    711  * We recommend not removing duplicates from any of the samples.
    812  * 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.