Output files
All the result files will be in a directory named by the parameter -o. It is result/ by default.
For each pair of comparison, e.g., A:B, the output directory result/ may contain the following files:
(1) A-B.regions.integrative.xls This file contains the protein binding regions defined in A and B, along with data generated by comparing each region between A and B. It contains the following columns:
chr Chromosome name
start the start point of a region
end the end point of a region
center the middle point of a region
control_height the maximal value of protein occupancy in a region in data B
treat_height the maximal value of protein occupancy in a region in data A
height_log2FC log2 fold change between treat_height and control_height
height_diff_log10Pval log10 P value for difference between treat_height and control_height. P value is calculated based on Poison test.
height_diff_FDR FDR value for difference between treat_height and control_height
control_width the number of base pair with occupancy value greater than cutoff within a region in data B
treat_width the number of base pair with occupancy value greater than cutoff within a region in data A
width_log2FC log2 fold change between treat_width and control_width
width_diff_log10Pval log10 P value for difference between treat_width and control_width. P value is calculated by Proportion test.
width_diff_FDR FDR value for difference between treat_width and control_width
control_total_signal the sum of occupancy values within a region in data B
treat_total_signal the sum of occupancy values within a region in data A
total_signal_log2FC log2 fold change between treat_total_signal and control_total_signal
total_signal_diff_log10Pval log10 P value for difference between treat_total_signal and control_total_signal. P value is calculated by Poison test.
total_signal_diff_FDR FDR value for difference between treat_total_signal and control_total_signal
local_gain_log10Pval the log10 P value for maximal occupancy increase in data A relative to B at each base pair within a region. P value is calculated by Poison test.
local_gain_FDR the FDR value for maximal occupancy increase in data A relative to B at each base pair within a region
local_loss_log10Pval the log10 P value for maximal occupancy decrease in data A relative to B at each base pair within a region. P value is calculated by Poison test.
local_loss_FDR the FDR value for for maximal occupancy decrease in data A relative to B at each base pair within a region
local_change_log10Pval the maximal value of local_gain_log10Pval and local_loss_log10Pval.
local_change_FDR the minimal value of local_gain_FDR and local_change_FDR
(2) result/pooled/A....wig and result/pooled/B....wig These .wig format files contain protein occupancy values at each base pair across the whole genome in data A and B, respectively. Click for help information about .wig format
(3) result/pooled/A….regions.xls and result/pooled/B….regions.xls These files contains the protein binding regions defined in data A and B, respectively. Each file contains the following columns:
chr Chromosome name
start the start point of a region
end the end point of a region
center the middle point of a region
width_above_cutoff the number of base pair with occupancy value greater than cutoff within a region
total_signal the sum of occupancy values within a region
height the maximal value of protein occupancy in a region
height_logP The Poison test P value for height. P value is calculated by Poison test.
(4) result/pooled/A….refregions.xls and result/pooled/B….refregions.xls These files contains the protein binding regions (reference regions) that are either defined by integrating all the regions defined in each data set or provided by the -rf parameter. Values in each file are defined based on a single data set. Each file contains the following columns:
chr Chromosome name
start the start point of a region
end the end point of a region
center the middle point of a region
width_above_cutoff the number of base pair with occupancy value greater than cutoff within a region
total_signal the sum of occupancy values within a region
height the maximal value of protein occupancy in a region
height_logP The Poison test P value for height. P value is calculated by Poison test.
(5) result/diff/A-B…..wig This .wig format file contains a value indicating occupancy difference at each base pair between data A and B. Briefly, for each base pair, if occupancy value is greater in A relative to in B, the value in this file will be -log10 P value, else, it will be log10 P value. Click for help information about .wig format
(6) result/diff/A-B…..local_gain.refregions.xls and result/diff/A-B…..local_loss.refregions.xls These files contains the protein binding regions (reference regions) that are either defined by integrating all the regions defined in each data set or provided by the -rf parameter. Values in A-B…..local_gain.refregions.xls are defined based on all positive values in A-B…..wig, Values in A-B…..local_loss.refregions.xls are defined based on all negative values in A-B…..wig.