determination of --p-trunc-len and --p-trim-left

[tuyick (Patrick)]

Hello,

I'm still learning qiime2 with tutorials but I'm confused how i can choose the values for --p-trunc-len and --p-trim-left in the following case and the reason behind.

Thank you for your support

LogMPIE.qzv (307.6 KB)

[crusher083 (Valentyn Bezshapkin)]

Hello, Patrick!

Don't worry, learning is a continuous process! There is no hardline in this question, it is somewhat subjective.

In the figure, you might see some lower-quality bases in the beginning, which will define your --p-trim-left parameter. I'd say they level off at around 30bp, but I don't have interactive information

In the end, some low-quality bases are evident at around 220-230 bp. They will define --p-trunc-len parameter.

Cheers,
Valentyn

[tuyick (Patrick)]

Thank you very much @crusher083

[Keegan-Evans]

@tuyick,
You might want to checkout this video from one of our workshops that has a bit more of an in depth discussion of this topic.