9  Internal barcodes not removed

Figure 9.1: Sasha just can’t get any work done while the office keeps blasting 10 different songs at once! By Petra Korlević

Figure 9.2: Example of a smiley plot of a double stranded library with barcodes that were not removed prior mapping. Data taken from library GEN72 (ERR2112579) of (Andrades Valtueña et al. 2017). Damage data generated using DamageProfiler and plotted using R and tidyverse packages (Wickham et al. 2019).

In this case, this smiley plot is not very smiley as the mapped reads have not had ‘internal barcode’ removed prior mapping. As a side effect, you see a very spiky initial ‘curve’, and then the rest of the read being flat.

In this case, this library only has a single barcode on the 5p end, but some labs may add internal barcodes to both ends of molecules.

Andrades Valtueña, Aida, Alissa Mittnik, Felix M Key, Wolfgang Haak, Raili Allmäe, Andrej Belinskij, Mantas Daubaras, et al. 2017. “The Stone Age Plague and Its Persistence in Eurasia.” Current Biology: CB 27 (23): 3683–3691.e8. https://doi.org/10.1016/j.cub.2017.10.025.

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.