How do I analyse my microbiome run 150x2 with 9nt overlap in dada2 denoise_pair, if overlap default is min 12nt?

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1

Hi,

I have a Illumina run (150x2 v2) and amplicon size is 291, with a overlap of 9nt. I cutoff my primers/adaptors and I use dada2 (denoise_pair) to denoising sequences. In january, I can use this comand with --p-min-overlap 4 to change the overlap default into 4nt.

qiime dada2 denoise-paired
--i-demultiplexed-seqs demux-paired-end.qza
--p-trunc-len-f 150
--p-trunc-len-r 150
--p-min-overlap 4
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza

Now, I can´t use again, I have this error message:

There was a problem with the command:
(1/1?) no such option: --p-min-overlap

Why can I use this before, and not now? Is there a new tool to perform this analysis?

2

Hi @c_malossi,

I'm assuming you're doing 515F-806R 2x150 sequencing?

It's pretty widely accepted to just use forward reads for this purpose, so no need to modify the trim length. Here's a more detailed forum post on the issue:

Best,
Justine

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