Importing MRDNA fasta + qual files with merged R and F reads into qiime2

[llenzi (Luca)]

Hi @Hui_Yang,

please see this thread:

Can prejoined sequences be used for Dada2 pipeline

Hi, I am a beginner for Qiime2 and after reading the tutorials I started analyzing my data. I got OTU table after applying Dada2 pipeline and I noticed that merging for most of the samples have failed . As a result I lost most of the samples from otu table. Could you please provide your expert opinion on improving the parameters for getting all samples. I used following commnads qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --p-trim-left-f 25 --p-trim-left-r 20 --p-trunc-len-f 3…

You should be able to find the command for importing the sequences in your case!
Cheers
Luca