I have data from 16S rRNA sequencing, paired-end from v4 region. The sequencing is done at 2 x 150 read length.
I used DADA2 to merge them but came up very few sequences are left to process for downstream analysis, then I’ve been troubleshooting and found with my 815F&806R primer at 2x150 read length my overlap region is going to be only 4 to 5 nucleotide and wonder if this is the reason for having very few sequences left after merging?
How should we merge R01 and R02 in my situation? I read some discussion on google saying the forward and reverse fastq files contain reads in matched order. Does anyone know what does reads in matched order? if it’s matched when sequncing can I just merge my R01 and R02 with
mergePairs(..., justConcatenate=TRUE in R. And can we do the same in Qiime?