Help with making peaks MACS Chip-sequence analysis

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Hi @michele_palermo

Use MACS2 Callpeak and with all of the current default settings, except for these:

  1. ChIP-Seq Treatment File → select Bowtie2 treatment bam
  2. Do you have a Control File? → Toggle yes/no, select Bowtie2 control bam (if you have one, otherwise leave the toggle at “no”)
  3. Effective genome size → toggle the pull down menu to select M. musculus
  4. Set upper mfold bound → the default is now 50, which might be ok, or you can set this at 32. maybe try both and compare?

We have an updated versions of these tutorial available at the GTN. See the Epigenetics category. One example is here, and it involves paired-end instead of single-end data but is otherwise very similar. Formation of the Super-Structures on the Inactive X

Hope that helps!

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