DANPOS_v3.1

This is a repository with a corrected and updated version of Danpos.

DANPOS v3.1 is based on DANPOS3 from Samantha Klasfeld from the Wagner lab at the University of Pennsylvania.

For general usage and documentation check out README_Danpos3.md (README from DANPOS3) and/or ReadMe_Original.md (README from DANPOS2).

TLDR

Following changes were introduced to original DANPOS3

1. corrected determination of point of greatest difference in a nucleosome
2. all statistical tests are now based on scipy instead of R
3. shortened naming scheme of output files

Changes

1. There was a problem in determination of the point of greatest difference in a nucleosome. Therefore the XYZ.positions.integrative.xlsoutput had incorrect values in:

   • diff_smt_loca, control_point_val, treat_point_val, point_log2FC, point_diff_log10Pval, point_diff_FDR

2. The implementation of fishers and poisson-test in python introduced by danpos3 sometimes throwed errors and additionally they were not used in all instances in the code. The corresponding functions were fixed and their usage was impemented in all instances. This decreases runtime significantly. Unfortunatelly the resulting log10(pvalues) are capped at -308 due to python float precision. Lower pvalues are now returned as -Inf.

3. The naming scheme of output files resulted in very long base-filenames when input files were inside of a folder structure. For example input file path/to/file/input.bam resulted in output file path_to_file_input as a basename. This is changed to just input as a basename.