Need help deciding parameters for dada2 step

The reads are from Illumina for 16s (v1-v3) region. I have an output file attached from demux summarize for my data. Given the quality of the data, I wonder if I would be able to obtain overlap after the denoting step! I was thinking to use the below command, please suggest if that is okay or I could modify that.
qiime dada2 denoise-paired **
--i-demultiplexed-seqs demux.qza **
--p-trim-left-f 20 **
--p-trim-left-r 20 **
--p-trunc-len-f 280 **
--p-trunc-len-r 220 **
--o-table table.qza **
--o-representative-sequences rep-seqs.qza **
--o-denoising-stats denoising-stats.qza

Hi @shah,
A lot of discussion has occurred on this forum regarding trimming parameters, especially for V1-V3! So I recommend looking at those for more ideas. Your parameters look fine though I don’t know the actual length of your V1-V3 amplicons (depends on the primers and if primers have been trimmed already or not; if they are trimmed, don’t bother with the trim parameters).

That’s usually the biggest issue — I recommend just seeing if this works and checking the dada2 stats to see how many reads are dropping off at merging. If you have lots of merge failures, bump up the truncation lengths and try again.

I hope that helps!

1 Like

Thanks a lot. I am going to try that. Will keep updated. Thanks again.

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.