DADA2 truncation

[lizgehret]

Great follow-up questions @ek_97! Happy to address these below.

@ek_97

Wouldn't the --p-trunc-len discard all the sequences greater than this value since this command would be truncating the right side? So if I set the value to 150, wouldn't that get rid of all the bases above the 150 position, and not below?

You're exactly correct, good catch! I'll make sure we get that documentation updated.

@ek_97

In addition, what happens if I set the value of --p-trunc-len to higher than the whole sequence length? For example, if my whole sequence is around 150 bases, but I don't know the exact length, so what if I set the value to 151? Would it not truncate anything if my base was shorter than 151?

That's correct - your sequences will be left untouched if you specify a length in --p-trunc-len that doesn't have any reads greater than the given value.

For example, if my whole sequence is around 150 bases, but I don't know the exact length, so what if I set the value to 151?

Calling out this specific question, I'd recommend utilizing view.qiime2.org with the associated .qzv from your DADA2 analysis to determine what the length of your reads are. This information can be found under the interactive quality plot tab, which may also be useful for you when determining whether or not you need to trim/truncate your sequences due to a drop in quality.

I go into further detail on this tool, and some more specifics of the --p-trim-left and --p-trunc-len parameters in this forum post, which you may find useful as well.

Cheers,
Liz