Now I have 15 paired data(300bp, illumina) with 515FB(19bp) and 926R(20bp).
Here are my scripts and my results:
Importing data Casava 1.8 paired-end demultiplexed fastq
qiime tools import
qiime cutadapt trim-paired
qiime dada2 denoise-paired
And I have some questions:
- Why did the length of reads remain unchanged after primer trimming? They are still 300bp?
- In the first figure, the interaction quality plot of forward reads, why are there some missing parts (I mean only some dotted lines) at the beginning?
- My overlap= 2*300-(916-515)=189 (Here I do not know if I need to cut primer, because question 1), my trim= (300-246)+(300-226-5)=123, so it seems okay. But the percentage of input passed filter and the percentage of input merged is very low, even if I set: --p-trunc-len-f 243 \ --p-trunc-len-r 196 , it can only increase from 70% to 75%, but still very low, right?
I would appreciate any suggestions. Thanks!