The number of features is normal but the number of observed_otus is too low?

[ben (benjamin w.)]

Thanks, I noticed you have lost a lot after merged sequences to non-chimeric.

I think just reviewing this would be interesting (you're losing up to 75% of your reads between merged / non-chimeric.

This may explain why you los resolution. I sometimes lose up to 50% of the reads, but I think that's a lot of reads to lose on the last step.

As you can see, I don't lose a lot of sequences between merged and non-chimeric. See this:

loss of reads after DADA2 as chimeras

Hi, I am loosing around 70% of my reads as chimeras. Is my truncation parameters right ? or is it due to some other issues? demux.qzv (291.6 KB) My parameters were qiime dada2 denoise-paired \ --i-demultiplexed-seqs analysis/demux-paired-end.qza --p-trim-left-f 7 --p-trim-left-r 7 --p-trunc-len-f 298 --p-trunc-len-r 256 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza This was the denoising stats denoising-stats.qzv (1.2…

Also try here:

Dada2 filtering out >80% of reads as chimeras!

The adapter shouldn't actually be necessary to know as those sequences flank your primers which you do (or at least should) know. So if you trim everything before your forward primer and everything after your RC'ed reverse primer, you will remove all non-biological sequence

Ben