The nuc_contact_map command is used to create Hi-C contact map graphics from NCC format files.

nuc_contact_map [-h] [-o SVG_FILE_TAG] [-w SVG_WIDTH] [-s BIN_SIZE] [-m MIN_CONTIG_SIZE] [-b] [-c RGB_COLOR] [-ca RGB_COLOR] NCC_FILE [NCC_FILE ...]

NCC_FILE Input NCC format chromatin contact file(s). Wildcards accepted

-h, --help
Show command line options and exit

-o SVG_FILE_TAG
Optional name tag to put at end of SVG format contact map file. Use "-" to print SVG to stdout rather than make a file. Default: "_contact_map"

-w SVG_WIDTH
SVG document width

-s BIN_SIZE
Sequence region size represented by each small square (the resolution) in megabases. Default is 5 Mb

-m MIN_CONTIG_SIZE
The minimum chromosome/contig sequence length in Megabases for inclusion. Default is the bin size (see -s option)

-b
Specifies that the contact map should have a black background (default is white)

-c RGB_COLOR
Optional main color for the contact points as a 24-bit hexidecimal RBG code e.g. "#0080FF" (with quotes)

-ca RGB_COLOR
Optional color for ambigous contact points as a 24-bit hexidecimal RBG code e.g. "#FF0000" (with quotes)