this is my first experience with Qiime2. I try processing fungal ITS data. I have demultiplexed and trimmed data. As I understood it is Casava 1.8 paired-end demultiplexed format (my data: 1K1_S1_L001_R1_001.fastq.gz 1K1_S1_L001_R2_001.fastq.gz). I have 45 samples.
But after denoising by dada2 32 of 45 samples have Feature Count zero. Also when I checked denoising-status I saw that a half of samples haven't married sequences. I need chose sample depth for diversity analysis and if I exclude all samples with depth 0, there will left only 13 samples.
I've already tried changing the values of p-trim-left and p-trunc-len but it didn't help, the result was same.
qiime tools import
qiime dada2 denoise-paired
I suppose that I made mistake in the denoising step, because table with denoising status looks very strange, or may be I need another plugin for denoising. Please explain me what I did wrong.
Can anyone help me?
Thanks a lot!