The gamtools radial_pos tool is used to calculate chromatin radial positioning from GAM segregation tables. Radial positioning is estimated from the average size of NPs that contain a given chromatin region, since chromatin that occupies a more peripheral position will be intersected by smaller, more apical NPs (i.e. those which slice the nucleus close to the top/bottom/sides), whereas more central chromatin can only be intersected by larger, more equatorial NPs (i.e. those which slice the nucleus through the middle).

The size of each NP is estimated from it’s genomic coverage, i.e. the number of positive windows. NPs which contain a larger number of positive windows are assumed to also be larger in volume.

Usage and option summary


gamtools radial_pos [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)