I have sequencing data (300 bp) of V3-V4 region. I received this data from illumina through casava files means every zip file is already named with R1 and R2. I did not receive any barcode file from seq facility. I am not sure it is multiplexed or demultiplexed. I imported this data to qiime. The process was smooth and checked the read quality. AFter this, i used dada2 for denoising of only forward reads as i was facing problem with merging of both forward and reverse reads due to truncation length. After denoisng, i receive more than 900 features and 1 million frequencies. I was happy that i got good features as comapre to merged reads but then i checked that all the features belong to one sample.
I do not understand why it happens like this and how can i resolve this problem.