I've paired end 16s metagenomic data. I tried to join forward and reverse reads with
join_paired_ends.py but 50% data was assembled and I'm loosing 50% of my data which comes in
fastqjoin.un2.fastq. I think my reads are not overlapping there must be gap between two reads.
In this case how can I analyse metagenomic 16s data, since most of the metagenomic analysis tools accept single end data (eg. QIIME).