MACS2 peak calling

Question

[Maurice]

Hi all!

I have performed peak calling using MACS2. Is it correct that the bed file has not strand of the peak?

Thank you very much for your help

Answer 1

[ATpoint]

Yes, that is correct. Peaks from experiments such as ChIP-seq or ATAC-seq are based on DNA, which is double-stranded and unlike RNA (where we have expression from a specific strand) not strand-specific.

[Maurice]

Thank you! And for what regards peaks annotation, how can the tool I'm going to use assign peaks to the correct location without knowing the strand of the peak?

[ATpoint]

You do not need strand information for this as, as I said, strands do not apply in DNA-seq.

[seidel]

What ATpoint said. But given that, getting the distance between features depends on the tool you're using and how you ask questions. The "correct location" is simply a point on a numbered line of bases, regardless of strand. If you want to ask questions about distance between your peak and other features, make sure you know how your tool compares stranded and nonstranded features.