macs2 refinepeak Output File

[ara...@bu.edu]

Hi,

I'm running a "macs2.real refinepeak" command to define summit positions for a BED file of peak regions.  I have a question about the resulting output file from this command: in the peak ID column is there any meaning to the "_R" or "_F" that is appended to each peak ID?  

For instance, here is a sample of my input file:

chr1 3406264 3406744 female_27h_peak_1 0 TAD0_chr1begin

chr1 3445487 3446302 female_27h_peak_2 0 TAD0_chr1begin

chr1 3468181 3468500 female_27h_peak_3 1.1 TAD0_chr1begin

chr1 3504478 3505505 female_27h_peak_4 0 TAD0_chr1begin

chr1 3541383 3541610 female_27h_peak_5 0 TAD0_chr1begin

Here's a sample of my output file:

chr1 3406465 3406466 female_27h_peak_1_R 46.93

chr1 3445981 3445982 female_27h_peak_2_R 44.97

chr1 3468185 3468186 female_27h_peak_3_R 87.94

chr1 3505026 3505027 female_27h_peak_4_R 382.95

chr1 3541701 3541702 female_27h_peak_5_R 9.98

Note: the 4th column has the additional "_R" added to each peak ID.

I'm aware the score (last column) is defined here:

refinepeak: (Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP.

Does "_R" or "_F" mean reverse or forward respectively?  Is this something users should record or it is okay to ignore this information if we just want to know the summit for our called peaks?

Andy