MACS2 default peak type

[bounlu]

Your document says here:

MACS2 is run by default with the --broad flag.

However, MACS2 document says the opposite here:

--broad If set, MACS will try to call broad peaks using the --broad-cutoff setting. Please tweak '--broad-cutoff' setting to control the peak calling behavior. At the meantime, either -q or -p cutoff will be used to define regions with 'stronger enrichment' inside of broad peaks. The maximum gap is expanded to 4 * MAXGAP (--max-gap parameter). As a result, MACS will output a 'gappedPeak' and a 'broadPeak' file instead of 'narrowPeak' file. Note, a broad peak will be reported even if there is no 'stronger enrichment' inside. DEFAULT: False

Which one is correct?

[drpatelh]

We use the --broad setting in MACS2 by default for this pipeline because that tends to be better suited to the variable peaks sizes you have with ATAC-seq data. MACS2 itself doesn't use the --broad setting by default. They are both correct!

We could maybe clarify that sentence to MACS2 is run by default with the --broad flag in this pipeline. if it helps?

[bounlu]

Thanks for the clarification. Yes, that may help others.

[JoseEspinosa]

Answered 😄