I have forward, reverse and extended illumina myseq 16s rRNA v4-v6 amplicon reads. Length of v4-v6 region is about 520-530 bp while my forward and reverse reads length is only 250 bp each. I checked all three of them in fastqc and it appears that forward read is the best. Should i use forward read for classifying or it is better to use an extended, even if it has worse quality.
p.s. How is it possible to get an extended file when forward and reverse reads are not enough long for crossing? And why extended read quality is so bad in the end? Does not the merged file should have a degradation in the middle?
Fastqc reports attached (i don't know how to add html file properly, so i just added these links, sorry for that):