I am new here and I’ve read lots of posts about dada2 parameters but I couldn’t find any answer for me.
I used 515F–806R primers to get amplicons. Samples were extracted from chicken feces swabs. Reads are paired-end 2x300bp. Running QIIME2 2020.6 in a conda environment.
Based on the quality score plot above, I used the following code in the Dada2 step:
qiime dada2 denoise-paired /
–i-demultiplexed-seqs new-analysis-kit_comparison/pe-kit-demux_kit1.qza /
–p-trim-left-f 0 /
–p-trunc-len-f 260 /
–o-representative-sequences rep-seqs-kit1.qza /
–o-table table-kit1-dada2.qza /
–o-denoising-stats stats-dada2-kit1.qza /
–p-n-threads 0 /
As you can see on stats data file, I think I had a good filter and merge results, but I got a low percentage of input non-chimeric, which I think means that I lost 90% of my data.
Any clue on what is happening?
Thanks in advance
demux-kit1.qzv (316.1 KB)
stats-dada2-kit1.qzv (1.2 MB)