I am learning to use Qiime to analyze 16S V3/V4 sequencing data from the Illumina Miseq (PE 2x300).
I'm wondering if there is any regular convention in deciding whether or not to pair ends before processing data. Because the second read from the Illumina 600v3 2x300 gives you poor quality after 200-250 bases, it seems that there would be many reads that don't get paired if using any kind of pairing program, right?
Is it possible to simply merge the two fastq files for read 1 and 2, or would that not work because of directionality?
I was going to use multiple_split_libraries_fastq.py, but if I have read 1 and 2 separate, that won't work either, correct?
Thanks in advance for any information!