Hi @lizgehret
Following your clues I made a denoising with just the forward sequences, so I runned a dada2-single end. And this is my results, as far as I could interpret I don't think I missed much but it's strange, my percentage of input filtered aroun 40% in all of my samples, can you check and give me your opinion if the results are useful?
rep-seqs.qzv (938.5 KB)
stats-dada2.qzv (1.2 MB) table.qzv (1.1 MB)
Additionally I found in this forum > Blockquote Dada2 denoise - why do I have so many reads filtered out - #8 by Jo_mee, recommended by you, that V3-V4 2x250 runs, that is my case, often the reverse reads are not used. Why does this happen? I'm curious to try the denoising with my forward and my reverse reads. For the dada2-single end I used:
qiime dada2 denoise-single
--i-demultiplexed-seqs single-end-demux.qza
--p-trim-left 65
--p-trunc-len 230
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza
--o-denoising-stats stats-dada2.qza
I'm thinking about applying the same trim and trunc values to my reverse reads, what do you think? It will be useful or would be wasting time?
Thanks