Tutorial

Here is a collection of tutorials for MACS3.

• Advanced Step-by-step peak calling using MACS3 commands
  • Step 1: Filter duplicates
  • Step 2: Decide the fragment length d
  • Step 3: Extend ChIP sample to get ChIP coverage track
  • Step 4: Build local bias track from control
  • Step 5: Scale the ChIP and control to the same sequencing depth
  • Step 6: Compare ChIP and local lambda to get the scores in pvalue or qvalue
  • Step 7: Call peaks on score track using a cutoff
• Cutoff Analysis