My data (Fastq: paird-seq) has been uploaded successfully （qiime tools import
--type 'SampleData[SequencesWithQuality]' \）according to the instructions and demultiplex. the view of the demux.qzv shows that the complete 33 samples of this study
but after data denoising by dada2 the number of samples only have 28
I can't find why！please help me ！thanks you much！
at first glance the, run looks good. My only question is if are you cropping the pictures?
Because from them the sequences lengths seem to be less than 200bp to me, and if so, make sense that the truncation lengths you using left very few reads to work with.
Did you look at the denoising stats? It is always a good place to start to see what is happening during the denoising step. Another question is, which region are you amplifying? Make sure you still have at least 12-15 bp of overlap between R1 and R2 when you chose the truncating length.
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