Figures and plots for integration of ATAC and RNA seq data

Question

[SpartanII]

Hello all,

I was wondering what type of figures and plots people make and what values they graph. In papers I've been seeing a some of them plot lf2c and make heatmaps or scatterplots. Are there any other figures that would be interesting or better? If anyone has any ideas please let me know. I'm new to this and have no idea where to start.

Thanks

Answer 1

[jared.andrews07]

Depends entirely on what point you're trying to make. Figures are evidence to support the claims you're making. This is part of constructing a compelling scientific narrative, i.e. an article.

Based on the data and analysis results, come up with a one sentence claim that you want to make. Determine which figures would make that claim the most believable and then produce them. This requires you to put yourself into the shoes of the reader (and reviewer) - what questions would they have, what other mechanisms or artifacts or quirks in the data may be ghosts that seem to support the claim you're making but really don't, etc. Coming at the claim from multiple angles will help you to construct strong figures.

Ideally, a lot of this should be done before the work is even started. What questions does one what to answer - what data and analyses would be necessary to do so?

Just doing experiments and trying to piece together a narrative from the results post-hoc is a frustrating and slow way to do science. Be targeted, be smart with exploratory experiments, and always look for ways to validate computational findings as directly and easily as possible. Well-designed experiments with clear phenotypic outputs are much more convincing than most analyses.