The desktop version of the Integrative Genomics Viewer (IGV, The Broad Institute) is the best tool for making publication-quality browser tracks. The web-based version on CUTANATM Cloud is an excellent tool for assessing top-line data quality and experimental success without the need to download and manage all of your bigwig files. However, it lacks a number of critical features for figure generation, notably the ability to group autoscale tracks, save sessions, and set custom colors. You can download the desktop version of IGV at https://igv.org/doc/desktop/.
How do I make publication-quality browser tracks?
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