Help with making peaks MACS Chip-sequence analysis

I am part of a Coursera class and the then-professor has now passed so I cannot ask questions. The sequence that he showed is no longer applicable. So the question is after running Bowtie2 on a data set. I am using the demo data for mouse G1E_CTTCF. The parameters he had set were a tag size of 36 and an MFOLD of 32. The issue is the original peak calling is gone now and now closest is the MACS2 call peak but it does not have any of the same input options. So how would this workflow be reworked properly? I need this knowledge to be able to apply it for my final project and the chapter exam .

  1. Go to: **Tools
  2. Go to: NGS: Peak Calling
    3. Go to: MACS
  3. Go to Middle Panel:.
  4. Go to: Experiment Name:
  5. Mouse - MACS G1E_CTCF
  6. Tag File: Bowtie2 on data #: aligned sorted BAM
  7. Tag Size: 36
  8. Leave MFOLD: 32
  9. Check: Perform the new peak detection method (future dir): YES
  10. Execute
  11. This will produce two files:
  12. MACS on data 5 (peaks:bed)
  13. MACS on data 5 (html report)
  14. Click on View data (Eye icon) to get more information.
  15. Download from the html report data set:

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!