Huge loss of data while merging in DADA2.

I have 16S paired end 300bp length and primers are already removed. I tried to merge and denoise them using DADA2.
please find my interactive quality plot.

Here is my DADA2 command used:
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux-newdata.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 0 --p-trunc-len-r 0 --p-min-fold-parent-over-abundance 9 --o-representative-sequences rep-seqs-dad2.qza --o-table pet-table.qza --p-n-threads 1

Here is my denoising stats.

There is a huge loss while merging the data. Overall, quality of data looks fine. I am not sure why they failed to merge. Kindly help me in choosing truncation parameter. Do I have to change Qscore limit.

What 16S primer set are you using, and how long is the region?

If it’s 590+ bp then it would not be a surprise that the reads are failing to merge, if it is way less than 550 bp, especially if it is less than 300bp then some strange behavior would not necessarily be surprising.

If keeping both at 300 bp does make sense you may want to run the forward reads as single end, and make sure there is not anything surprising in your data (such as host amplification if you have a gut sample)

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