Genome Browser Figure
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12.7 years ago
Egl ▴ 20

I would like to create a nice figure illustrating, for example, different histone modifications on a given region. An example of what I wish to create is the supplied figure, which is from a random article.

My workplace has previously used Nimblegens SignalMap browser. SignalMap produces quite nice end results, but is rather cumbersome to work with.

I have looked into IGV, which seems a lot more advanced, but I haven't yet been able to create as nice figures with it as with SignalMap.

I'm wondering what's the most popular general purpose genome browser around (for mammalian genomes). Is it common to use the genome browser to produce article quality figures?

edit: I was unable to insert the picture, I'll try to link it instead.

genome igv visualization • 11k views
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12.7 years ago
Ido Tamir 5.2k

I am quite confident that the figure was brushed up with a graphics program. None of the genome browsers I know have this nice positioning of the track descriptions at the right within the track. The scale on the left also shows just the maximum and no 0, I guess most browsers show some tick marks in between. If you want a really nice figure, you need to save the output of a genome browser as SVG or PDF (PS) and rework it a little bit e.g. inkscape or adobe illustrator.

The most popular is I guess UCSCs genome browser, but popularity does not equal nice figures.

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12.7 years ago

From UCSC genome browser you can export to PS or PDF (click PDF/PS in the top bar) and then edit with a vector graphics editing program like Illustrator or Inkscape. I would recommend tweaking the browser settings to remove light blue gridlines prior to export.

From IGV you can export a few types of images, including svg, but I personally don't think the figures end up looking as good.

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4.6 years ago
bernatgel ★ 3.4k

Since this question has been resurrected, I'll add karyoploteR to the list of available tools. It's an R/Bioconductor package to plot data on genomes and can work with BAM files or BigWigs (and many other formats, actually).

At the turorial page you can find an example on how to plot ChIP-seq data from histone modifications and DNA-binding proteins with complete step-by-step code to get to this final image.

enter image description here

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Great suggestion. Thanks!

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12.7 years ago
Bert Overduin ★ 3.7k

It is possible to add custom tracks to Ensembl.

If you have any questions and/or need help you're welcome to mail helpdesk@ensembl.org.

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12.7 years ago
Casbon ★ 3.3k

It's not a browser, but genometools produces really nice output: http://genometools.org/images/cnn_large.png

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4.6 years ago
ivar.grytten ▴ 40

I know this answer comes late, but I came over this question myself just recently searching for tools to do what you want (so I guess other people might do the same).

I've now tried a few tools, and from my experience these two work really well:

Example from the PyGenomeTracks repo:

enter image description here

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