1. peak list (*.cod) Column1: peak rank Col2: chromosome Col3: peak start Col4: peak end Col5: peak strand (currently all +) Col6: peak length Col7: maxN = maximal read count with a W bp window. W is the window width used to detect peaks. Col8: maxN_pos = the center position of the Wbp window that contains the maximal number of reads. Col9: total_reads = the total read count within the peak Col10: Ftot_reads = the total count of 5' reads Col11: FmaxN = maximal 5' read count with a W bp window. Col12: FmaxN_pos = the center position of the Wbp window that contains the maximal number of 5' reads. Col13: Rtot_reads = the total count of 3' reads Col14: RmaxN = maximal 3' read count with a W bp window. Col15: RmaxN_pos = the center position of the Wbp window that contains the maximal number of 3' reads. Col16: Rmaxpos-Fmaxpos = distance between 5' peak and 3' peak, i.e. RmaxN_pos -FmaxN_pos+1. Col17: Delta = [min(FmaxN, RmaxN)+1]/[max(FmaxN, RmaxN)+1] 2. peak signals ([your output file title].bar) Read counts in a W bp window. A sliding window with length W bp is used to scan genome at a step size S. S is specified by -s option in the hts_peakdetectorv2. Default S = 25 bp. *_F.bar are the window read counts for 5' reads. *_R.bar are the window read counts for 3' reads. Bar files can be visualized in CisGenome browser. If you want to examine them, you may use affy_bar2txt to convert them to text files.