150PE reads vs 250PE reads novaseq data

I am new to Qiime2 and bioinformatics and try to figure out a lot myself. Soon I will be able to collect my first data and send it for sequencing. It will be sequenced using Novaseq6000 paired-end 150 bp.
The qiime2 tutorials helped me a lot. However, I was reading in the Parkinson's mouse tutorial the following:
"The hypervariable region covered by the primers we used is 290bp long, so with 150bp reads our sequences will be slightly too short to be able to do paired-end analysis downstream"
This made me wonder whether the output that I will receive from my samples after NovaSeq Sequencing will also be too short to do paired-end analysis.
What would you advice me to do for my analysis? Paired-end or only use the forward sequences as in the mouse tutorial?

Hi @AnkeWigger ,
I would personally go for longer reads, since the likelihood of success is higher. 150 bp is cutting it a little too close for successful read pairing with dada2.

It depends on the run quality — so if you have already paid for this I'd say just wait and see. If you have very good quality you can try denoising without any truncation and see if the reads merge successfully.

Good luck!

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