I spend three days for reading the whole tutorial.
I imported my data with Casava paired-end format. In next step which is demultiplexing I must work with casava 1.8 paire-end format, but there is only EMP format.
My libraries have not been demultiplexed. I passed only Importing stage. That is all. By the way, each of library including treated and untreated samples. So absolutely I have to de multiplex them!
I am in demultiplexing step! My data were casava 1.8, not EMP.
I need demultiplexing command for casava 1.8. There is no plugin based on I received from Linux terminal. You told me I follow FASTQ manifest format, but in delmultiplexing step there are only two ways:
“Read more about demultiplexing and give it a spin with the moving pictures tutorial (for single-end data) and Atacama soils tutorial (for paired-end data). Those tutorials cover EMP format data (as described in the importing docs). Have barcodes and primers in-line in your reads? See the cutadapt tutorials for using the demux methods in q2-cutadapt . Have dual-indexed reads or mixed-orientation reads or some other unusual format? Pray hard 
. Then check out the QIIME 2 forum to see if someone has found a workaround.”
I did not find any demultiplexing plugin for Casava 1.8 paired-end!
Shall I follow demultiplexing for EMP paired-end format? If yes, how would it be valid while I started with Casava 1.8 paired-end?
Existing formats are Moving Picture and Atacama, not further more!
I got confused!