I imported pair-ends reads (PE300, Illumina HiSeq 4000 PE100, fastq files with quality at 33bp) with the manifest option reporting R1 as Forward and R2 as Reverse reads in 2 separeted column on top of the sample-id column.
qiime tools import
When I look at the demux-summay, I end it up with better quality of my reverse compared to forward reads. Any idea why? Should not be the contrary ?