we did a 16S RNA analysis using MiSeq kit version 3. This kit makes paired-end reads with a size of 300pb. By merging both reads, we can cover 535 pb of region V3-V5.
As you can see in the following plot, qualities of reads are really bad after the nucleotid 250. Is it normal ? Perhaps the strategy prefers reads lenghs to the quality ? Did you get something similiar with the same kit ?
After merging with Flash