Field of Science

Spacing analysis back on track

My wizard post-doc is teaching himself R and other useful tools for bioinformatics, and so was able to quickly generate a new DUS position dataset using my Gibbs-derived matrix, and use this to check the spacing. This showed the expected peak at very close spacings,n but I couldn't use his data for my figures because it wasn't derived the same way.

So I redid my analysis of my dataset - no peak. The I replicated the analysis on a different dataset, which gave the expected peak (good -this means the analysis method is fine), but I couldn't use this dataset for my figure because it was a bit too small - it had only 2872 DUS sites, but my analysis needed at least 2902. So I concluded that something must be wrong with the position labels in the original dataset, but couldn't figure out what this might be. I searched and searched my old analysis files (buried in various cryptic folders on my computer and on the Westgrid server, and finally found another one big enough to use. Analyzing it gave the expected peak, and now I have a nice figure showing the not-very-exciting result that the spacings of DUSs and USSs found by Gibbs analysis are like those originally reported for their perfect-consensus counterparts. But presenting this figure will set the framework for the analysis of the spacings of simulated uptake sequences, which I need to redo today (I think my runs have given me the data I need).

And today I need to print out the manuscript and work through it carefully; I've been focusing a lot on the data and not enough on what we should say about it.

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