I am using dbcAmplicons pipeline for my data analysis of 16s rRNA from microbial communities in chicken gut based on Illumina sequence. The logic is to use paired reads yet only about 2 % of my reads are paired, the rest are not. What could be problem? and what is the implication of working with this too few no of paired reads down stream? PS: I am just learning the basics of command language and hoping my question makes sense? i appreciate your help.
Thanks @toralmanvar for your response. I realized adapter sequences are only about 8bp yet my average library sizes is 500bp. The reads on Illumina MisSq was 2x151bp I realized that this may result in gaps when joining the paired end reads and may result in low joined read%?
Can you tell us which variable region you have sequenced? Because if amplicon size is more than 300 bp, and you have sequenced it on 2 x 150 bp chemistry, then they don't have any overlaping region to join. Thus, preferably 16s amplicons (specially v3-v4 region) are sequenced on 2x250 or 2x 300bp chemistry.