I ran into a problem of merging 2x150 bp V4 region paired-end reads produced by Illumina Iseq100. Primers used for sequencing are 515F–806R. As sequenced reads include primer sequences, the overlap of the reads is too small, which results throwing away a lot of reads while trying to merge. I have tried merging with DADA2 integrated into QIIME2 (dada2 denoise-paired, truncating only primer sequences, but nothing from 3’ ends) and vsearch (vsearch join-pairs with parameter “–p-minovlen 5”). For example in case of using vsearch from 503298 reads only 27033 (3,5%) remained after joining.
The solution I have found is to analyse this data as a single-end data, but in this case I lose half of the information I have regarding the sequences.
What are the possible solutions to still perform analysis with paired-end sequences and information from both of the reads, if there is any solution?
I am using QIIME 2 version 2019.1.0 command line interface installed with conda.
Thank you for your help!