Annotation/Alignment Visualisation Software For Use In A Presentation

Question

[Mattrition]

Currently I am using IGV to visualize the GFF files that I am creating. However, screen grabs of the viewer don't translate well to presentation slides and reports. Is there something similar around that might be a little less confusing when used in a presentation?

Answer 1

[Vitis]

Gbrowse does image dumps, but the resolution is not high, either. But you may give it a try.

[Scott Cain]

Not true--GBrowse can export SVG as well as pdf if the administrator has configured it to do so. While pdf export is still fairly rare (though not at all difficult to add), SVG export is quite common.

[Vitis]

I guess the developers always have better answers than me. You can also try standalone biographics rendering GFF, I found that pretty good, too.

Answer 2

[Casey Bergman]

If your data is from one of the organisms in the UCSC genome database, you can upload your annotation (as BED, GTF, etc) as a custom track, modify the display using the "Configure" image function, and export as a PDF or Postscript file using "PDF/PS" function at the top of the browser page.

[Bert Overduin]

And the same holds for Ensembl (http://www.ensembl.org).

Answer 3

[brentp]

Have you tried exporting from IGV as SVG? Then you should be able to resize and still keep crisp graphics and fonts.

From your description, it sounds like you're actually taking a screen grab with external software. If that's the case, you'll likely have better results using the built-in utility to save a screenshot. Just go to File -> Save Image ... (and then try SVG output.)

[Mattrition]

I've been using the save image option in IGV. My problem is more that IGV's visualisations aren't that intuitive. For example people had trouble working out where CDS features started and stopped. I have to do all my labelling afterwards in paint as well, since there's no way to add your own in the software (or give it an attribute from the GFF)