Introduction

D4 Plot displays D4 genomic signals. You can compare tracks, add GFF3/GTF/BED annotations, export bedGraph or SVG, and create coverage D4 files from BAM/CRAM.

Start with Start here.

Reading the plot

Each plotted value is the mean for a display bin, after applying any scale stored in the D4. Zoom in to inspect narrow peaks; a wide bin can hide variation.

Before comparing tracks, confirm their reference assembly, chromosome names, and data processing. D4 files do not identify their source assembly. Use Shared Y when comparing signal heights.

Viewer coordinates are 1-based and inclusive: chr1:100-200 spans 101 bases. Exported bedGraph intervals are 0-based and half-open.