The gamtools compaction tool is used to calculate chromatin compaction from GAM segregation tables. Chromatin compaction is estimated from the number of NPs that contain a given chromatin region, since chromatin that occupies a larger volume will be intersected by a greater number of NPs.

Usage and option summary


gamtools compaction [OPTIONS] -s <SEGREGATION_FILE> -o <OUTPUT_FILE>

Optional parameters:

Option Description
-n, –no-blanks Exclude regions that were never detected from the output (for making bedgraphs)