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.positions.integrative.xls This file contains the protein binding positions defined in A and B, along with data generated by comparing each position between A and B. It contains the following columns:
chr chrosome name
start the start point of a position
end the end point of a position
center the middle point of a position
control_smt_loca the occupancy summit point of a position in data B
treat_smt_loca the occupancy summit point of a position in data A
diff_smt_loca the point with biggest difference in occupancy in a position
treat2control_dis the distance between treat_smt_loca and control_smt_loca
control_smt_val occupancy value at control_smt_loca in data B
treat_smt_val Occupancy value at treat_smt_loca in data A
smt_log2FC log2 fold change between treat_smt_val and control_smt_val
smt_diff_log10pval log10 P value for difference between treat_smt_val and control_smt_val
smt_diff_FDR FDR value for difference between treat_smt_val and control_smt_val
control_point_val Occupancy value at diff_smt_loca in data B
treat_point_val Occupancy value at diff_smt_loca in data
point_log2FC log2 fold change between treat_point_val and control_point_val
point_diff_log10Pval log10 P value for difference between treat_point_val and control_point_val
point_diff_FDR FDR value for treat_point_val and control_point_val
control_fuzziness_score Fuzziness score for a position in data B
treat_fuzziness_score Fuzziness score for a position in data A
fuzziness_log2FC log2 fold change between treat_fuzziness_score and control_fuzziness_score
fuzziness_diff_log10pval log10 P value for difference between treat_fuzziness_score and control_fuzziness_score
fuzziness_diff_FDR FDR value for difference between treat_fuzziness_score and control_fuzziness_score
(2) reference_positions.xls This file contains a set of reference positions defined by integrating all the positions defined in each data set. It contains the following columns:
chr chromosome name
pos the middle point of each reference position
(3) 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
(4) result/pooled/A….positions.xls and result/pooled/B….positions.xls These files contains the protein binding positions defined in data A and B, respectively. Each file contains the following columns:
chr chromosome name
start the start point of a position
end the end point of a position
smt_pos the occupancy summit point in a position
smt_value the occupancy value at smt_pos
fuzziness_score the fuzziness score of a position
(5) result/pooled/A…..positions.ref_adjust.xls and result/pooled/B…..positions.ref_adjust.xls These files contains the protein binding positions defined in data A and B, but are further refined bake taking the reference positions into consideration.
chr chromosome name
start the start point of a position
end the end point of a position
smt_pos the occupancy summit point in a position
smt_value the occupancy value at smt_pos
smt_log10pval the P value for occupancy value at smt_pos
fuzziness_score the fuzziness score of a position (a larger score means more fuzziness)
fuzziness_log10pval the P value for fuzziness score of a position, a lower P value means better positioning (less fuzziness)
(6) 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
NOTE: In all these files, The P value for occupancy or occupancy difference is calculated based on Poison test, the P value for fuzziness score or difference in fuzziness score is calculated based on F test, as was described in:
Chen, K., Xi, Y., Pan, X., Li, Z., Kaestner, K., Tyler, J., et al. (2012). DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing. Genome Research. doi:10.1101/gr.142067.112