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

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)

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 :slight_smile:

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

Cheers,
Valentyn

1 Like

Thank you very much @crusher083

@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.

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