Publishing RNA-Seq Data

[Airwalker810]

Hey All,

We are attempting to sum up some of our RNA-seq data for publishing in a journal, and have run into an obvious problem: Screen Captures from the Integrated Genome Browser look like garbage in published work.

I was wondering what anybody else had been using to get work out the door. Something simplistic will do, but I need to be able to show gene models, as that is a crucial part of our work.

I suppose a decent example would be Figure 4 of this paper:

http://www.ncbi.nlm.nih.gov/pubmed/17346786

Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila. Brennecke et al.

The figure shows some gene model content (even if it smallRNA Seq), and something like this would look nice I think.

Thanks.

[GenoMax]

You are able to save images from IGV as "png" or "svg" format (file --> save image).

You may also be able to use exports from UCSC genome browser for the same purpose.

[Airwalker810]

Yea, we have been messing with image exports from IGV for awhile now, and they don't seem to stand up to the quality that we want. I was thinking of a more customizable sort of interface, where you can change labels, font sizes, etc, readily.

UCSC is not an option for us, as our servers have an issue with communication with the UCSC servers that both institutions cant seem to figure out.

Thanks

[arolfe]

I haven't tried this with IGV, but with other genome visualizers, I've exported as SVG and then opened the file in Inkscape (an Illustrator clone; SVG is its native format). You'll need to "UnGroup" madly, but then you can edit individual items to change colors, fonts, etc. You can also select and edit groups of items, eg, to change the size or color of a set of datapoints.

[puggie]

If you use UCSC GB you can export as pdf for Adobe Illustrator, and generate high-res pictures.