Ucallpeak - Comprehensive NGS peak calling from replicates

Image shows Ucallpeak peakcalls in first row, and MACS2 bdgdiff calls with different 
stringency settings below.


Expample Upeakcall output.



Usage:
Use sorted normalized bedgraph files as input.

Example:
python Ucallpeak.py \
-t treatment1.bed treatment2.bed \
-c control1.bdg control2.bdg control3.bdg \
-o output.txt

Required:
-o        Output file name
-t        Treatment files
-c        Control files

Optional:
-chr      only do analysis for this chromosome - can be used to parallelize the script
-e_bed    exclude all regions in this bed file
  

Known issues:
This script is not very efficient and will run for a significant time. 
It is reccomended to split up chromosomes (-chr command) to paralellize and speed up the analysis.