I have a question that seems to be relevant to this stream. I imported my raw data (16S V4V5, 515f/806r) using Casava 1.8 paired-end demultiplexed fastq format and they seem fine. Then I try to join them using vsearch command and I don’t think they are joined. Here are the qzv files.
csv18-joined.qzv (300.6 KB) csv18-pair-end.qzv (313.8 KB)
I used vsearch with default parameters:
qiime vsearch join-pairs --i-demultiplexed-seqs csv18-pair-end.qza --o-joined-sequences csv18-joined.qza
I also imported R_1 reads as single-end seqs and ran DADA2, which is what I usually do, on both single-end and paired-end seqs, and I got about half features from paired-end seqs than from single-end seqs.
I don’t know what is going on. Is this a problem with my sequencing data or some parameters I did not set right?