Dear forum memebers,
I need your kind help to figure out why I loose almost 90% of reads in 10 samples out of 30 after dada2 filteration step.
I did the calculations as follow
805-341 equals 464 length-of-amplicon
trunc-len-r + trunc-len-l - length-of-amplicon = overlap
280 + 200 - 464 = overlap
16 = overlap
16 bp gap!! 
Please see attached as ref. the quality of my forward and reverse reads.
Many thanks in advance.
805-341 equals 464 length-of-amplicon
trunc-len-r + trunc-len-l - length-of-amplicon = overlap
280 + 200 - 464 = overlap
16 = overlap
That's correct! The reads are expected to overlap by 16 basepairs.
(There is no gap, which is good!)
It looks like many of your reads are merging and there are thousands of reads in most samples, so this may be okay!
If I had data like this, I would continue with analysis and return to this step if I discovered issues later.
@colinbrislawn thank you so much for your quick response!
Unfortunately the 8 samples I loose at the dada2 filteration step is important for my study. They all have over 30k reads but turn into less than 1k after dada2 filteration step.
Any way I could diagnoise why I loose them although I should have enough overlap for merging?
