Just an Update and more questions!
I did the Demultiplex step according to this page (Demultiplexing and Trimming Adapters from Reads with q2-cutadapt).
As you can see in the attached picture, I demultiplex my samples based on my barcodes, but still, I have the adaptors which look fine to me, I just want to double-check it (this is my first question! Does it make sense (please see the picture).
My second question is about the next command:
Trim adapters from demultiplexed reads
If there are sequencing adapters or PCR primers in the reads which you’d like to remove, you can do that next as follows.
$ qiime cutadapt trim-single \
--i-demultiplexed-sequences demultiplexed-seqs.qza \
--p-front GCTACGGGGGG \
--p-error-rate 0 \
--o-trimmed-sequences trimmed-seqs.qza \
--verbose
Do I have to put the adaptor sequence in P front? for me it is GATACCTGCCTGCCG. Do I also need to remove reverse adaptor?
Last concern: I am following the steps provided by @thermokarst in this page ( Demultiplexing and Trimming Adapters from Reads with q2-cutadapt). Are these steps for Ion Torrent sequence (S5). I had seq fna file with qiime one but I decieded to redo all steps with Qiime 2 and the only page (steps) that were match with Ion torrent was this page (Demultiplexing and Trimming Adapters from Reads with q2-cutadapt) (I also imported my fastq file with this command: qiime tools import --input-path sequences.fna --output-path sequences.qza --type ‘SampleData[S
equences]’)