3  Partial UDG (double-stranded)

CARICATURE PLOT GOES HERE

Figure 3.1: Example of a smiley plot of a double-stranded ‘partial UDG’ or ‘UDG half’ library. Data taken from library VLI092.A0101 (ERR8958796) of (Andrades Valtueña et al. 2022). Damage data generated using DamageProfiler and plotted using R and tidyverse packages (Wickham et al. 2019).

The smiley plot presented here has been generated from a double-stranded ‘partial UDG’ or ‘UDG-half’ library. UDG or USER Treatment consists of enzymatically cleaving off ends of molecules when a uracil is present. Whereas complete-UDG UDG full runs the protocol long enough for all DNA molecules to be enzymatically modified, partial UDG stops early, meaning that a small number of reads retain uracils on the last base. This allows for simultaneous authentication of damage, but makes it easier to then in silico remove damage by ‘trimming’ off one base from either end of each read, so you can ensure you do not incorporate damaged bases into downstream analyses.

Andrades Valtueña, Aida, Gunnar U Neumann, Maria A Spyrou, Lyazzat Musralina, Franziska Aron, Arman Beisenov, Andrey B Belinskiy, et al. 2022. “Stone Age Yersinia Pestis Genomes Shed Light on the Early Evolution, Diversity, and Ecology of Plague.” Proceedings of the National Academy of Sciences of the United States of America 119 (17): e2116722119. https://doi.org/10.1073/pnas.2116722119.

Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the Tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.