NAME - Convert BED or extended BED files to bedGraph format

SYNOPSIS [-f FILE] [-c FILE] [-t STRING] [-a STRING] [options]


This program converts BED files to strand specific bedGraph files, allowing additional annotation and automatic generation of bedGraph files which can easily be converted to big-type files for UCSC visualization.



BED file for conversion.


File containing chromosome sizes


Type of bed file (e.g. sample name, replicate name, condition, ...)


Whether file is a standard bed or extended bed, 'extended' for extended bed

--help -h

Print short help


Prints the manual page and exits


Joerg Fallmann <>