1. peak list (*.cod)

rank: peak rank
chromosome: chromosome
start: peak start
end: peak end
strand: peak strand (currently all +)
peak_length: peak length
FDR: false discovery rate

--------Optional------------
If you have checked boundary refinement (or -br 1 in command line), then the following columns will provide more accurate peak boundaries for transcription factor binding sites. When you search for motifs, use these refined boundaries or extend from the refined peak summit.

left_peakboundary: refined left peak boundary, this is the mode of the + strand peak
right_peakboundary:  refined right peak boundary, this is the mode of the - strand peak
peak_summit: position with the highest signal
bound_center: (left_peakboundary+right_peakboundary)/2
bound_width: right_peakboundary - left_peakboundary + 1
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maxT: maximal window statistics in the peak
maxT_pos: position where the maxT is achieved
max_log2FC: maximal log2 fold change between normalized IP and control DNA fragment counts. Before computing the fold change, a pseudocount 1 is added to both the denominator and numerator.
maxFC_pos: position where max_log2FC is obtained
minuslog10_minPoisP: -10*log10(p-value). The p-value is obtained by the local poisson read sampling model. If "Apply Local Read Sampling Rate Filter" has not been checked, this column does not have meaning.
minPoisP_pos: position where the minimal p-value (or the maximal minuslog10_minPoisP) is achieved

--------Optional------------
If you have checked "Export Normalized Data" (or -dat 1 in command line), then the subsequent columns are normalized DNA fragment counts for each peak. Each column corresponds to a DNA sample (i.e. a *.aln file).
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2. peak signals ([your project title]*.bar)
*_log2fc.bar = this file saves log2 fold change between normalized IP and control DNA fragment counts for each bin. To save storage space, if -0.5<log2FC<0.5, then the log2FC will not be saved. 
*_t.bar = this file saves the window statistic T for each bin. To save storage space, if -1<T<1, then T will not be saved. 

Both bar files can be visualized using CisGenome browser.

Note: If you also want to visualize raw read alignments for each sample, you have to run "Sequencing > Alignment->BAR" to convert the ALN files to BAR files. You can then manually load BAR files into CisGenome browser as described in Tutorial 3.