# Why do the DADA2 default setting have such a low PHRED score? **URL:** https://forum.qiime2.org/t/why-do-the-dada2-default-setting-have-such-a-low-phred-score/10156 **Category:** General Discussion **Tags:** dada2, phred, quality-filter, quality-control **Created:** [June 10, 2019, 2:05pm UTC](https://forum.qiime2.org/t/why-do-the-dada2-default-setting-have-such-a-low-phred-score/10156 "2019-06-10T14:05:00Z") **Posts on this page:** 1 **Showing post:** 8
### Author: ![benjjneb](https://forum.qiime2.org/user_avatar/forum.qiime2.org/benjjneb/32/1602_2.png) [@benjjneb](https://forum.qiime2.org/u/benjjneb) #### Post date: [June 12, 2019, 12:28pm UTC](https://forum.qiime2.org/t/why-do-the-dada2-default-setting-have-such-a-low-phred-score/10156/8 "2019-06-12T12:28:33Z")
> [@SamWilliamsUOB](#): > > Why does the DADA2 default settings have the PHRED score set to 2? This seems far too low and as far as I understand it mean there would be a higher chance of the base being called in correctly than correctly? > > Despite this I rarely see any body alter the default quality cut off? Only the truncation length and trim parameters. Hi Sam, this is because the primary and recommended quality filtering parameter in DADA2 is "expected errors" (`max-ee`), which is based on the quality scores but is a better filter than averaging raw quality scores. You can read more about EE filtering here: [https://doi.org/10.1093/bioinformatics/btv401](https://doi.org/10.1093/bioinformatics/btv401) The quality truncation at q-score 2 is really just for older Illumina software where a score of 2 was code for "I don't know what's going on anymore" and any bases after the first 2 often were poor. These days, it's basically superfluous in most cases, and I'd recommend using `max-ee` as the quality filter in almost all cases, in conjunction with `trunc-len` to truncate off low quality suquence tails. --- _[View the full topic](https://forum.qiime2.org/t/why-do-the-dada2-default-setting-have-such-a-low-phred-score/10156)._