How to determine the values of trim parameters?

[KE_XU]

Hi, I have some trouble with understanding the quality scores plot for my data.

I am not sure how to determine the values of these four trim parameters?
--p-trim-left-f
--p-trim-left-r
--p-trunc-len-f
--p-trunc-len-r

Thanks in advance!

[cherman2 (Chloe Herman)]

Hello @KE_XU!
So basically you are currently looking at box-plots of quality for your sequences. You can click on point in the graph and see the median score of base X for all of your sequences. I cant really give you are rule for quality, A classic saying of the Qiime2 community "it depends" . Generally a median above or around 30 is good but again there is no "rule ".

The -f and -r refer to your forward and reverse reads.

For trim-left: This is looking at the beginning of your sequences. If you still have primers in your sequences then you will want to trim-left so that you remove the entire primer.

for Trunc-len: You are looking at the end of your sequences. you are looking for a fall off in quality and to truncate roughly right before the drop off. This is basically so dada2 doesn't get lost in the weeds of bad data. Also something to consider for joined end reads is that if you trim too far then you might not be able to merge them. (I don't think this will be a problem for you but keep that in mind).

Hope this helps!
Chloe