gamtools plot_np tool is used to plot the sequencing coverage and the
window calling output for a single NP over the whole genome. It can be very
useful as a quick quality control, as NPs that have been sequenced correctly
display a characteristic pattern of coverage, with many large regions (up to
whole chromosomes) displaying very low coverage.
Plotting the coverage for an NP requires three files, a bigwig file made from the raw sequencing data, a bed file containing the positive windows and a file containing a list of chromosomes and their lengths in bp (a genome file).
Usage and option summary¶
gamtools plot_np -w BIGWIG_FILE -b BED_FILE -g GENOME_FILE -o OUTPUT_FILE