bio-informatica: quality control 18S sequencing data

[slambrechts]

er een probleem met de combo DADA2 en het nieuwe binned quality scoring systeem dat Novaseq en Nextseq sequencers gebruiken (Zie o.a. benjjneb/dada2#1307.

• Test de 4 error learning methodes uit (die te vinden zijn in https://github.com/ErnakovichLab/dada2_ernakovichlab#learn-the-error-rates) die ontwikkeld zijn om dit probleem aan te kaarten, op onze 18S data, en kies de error plots die er het best uitzien voor onze data.

"you should carefully inspect the error plots generated by each method below and choose the one that looks the best. Error rate plots that look good have black points that are very close to the black line and are continuously decreasing (especially in the right side of the plot)."

you will notice a characteristic dip in the default error plots and you may have points that are far off of the line. This is typical and you will likely want to use one of the other options for error rate functions as simply increasing nbases will not solve this problem. There are four options, none of which will yield “ideal” error plots. Instead look for the solution where the black line is continuously decreasing (i.e. as quality scores improve on the x-axis the predicted error rate (y-axis) goes down) and for plots that have points that mostly align with the black lines, although you will likely have some points along 0 on the y-axis.

https://github.com/slambrechts/INBO_eDNA_metabarcoding_BODEM/issues/128