Obtaining high-quality figures from UCSC Genome Browser

The UCSC Genome Browser is widely used for genomic data visualization. Being a web-based application, it works in an internet browser like Firefox or Chrome and shows a schematic representation of a genome in low resolution that is enough for a screen. However, journals often require high-resolution figures for manuscripts to be submitted or published. The UCSC Genome Browser provides an opportunity to export such figures.

To download a current view of the genome browser, choose the menu item View > PDF/PS on the top of the browser webpage

ucsc_gb_menu_screenshot

and click on the link Download the current browser graphic in EPS.

ucsc_gb_eps_download

The downloaded EPS file can be inserted in a manuscript or converted to other format. For example, one may easily convert it to the PNG format using ImageMagick in the following way.

convert -density 600 figure.eps -background white -flatten figure.png

Note that we add the white background to the produced figure by specifying the following options: -background white -flatten, otherwise we would obtain a PNG file with a transparent background. Resolution (in dpi) of the output figure is given by the -density option. Below is the high-resolution figure obtained with the specified parameters.

ucsc_gb_high_res

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