Hi again @SoilRotifer,
Thank you so much for responding so quickly and in such detail! The truth is that it is great to have a forum where you can expose your doubts and receive such complete answers. My congratulations to the moderators! 
You are rigth. The quality control proccess should be as completed as possible. But I thougth that, maybe, I was adding redundant steps in the pipeline.
I admit I was wrapping my head around that. Thank you for suggesting these posts!! I am going to read these posts!!! 
Also, I would like to ask another question related to this. In a primer trimming with cutadapt, you use --discard-untrimmed to discard all the sequences without primers add in the cutadapt command of your data. But, how are you sure this parameter is working well?
I mean, for example, if your original sample files show a high number of reads and your cutadapt files:
- Show the opposite (poor number of reads in the count summary).
- Your cutadapt reads number be too similar to the original?
In these two cases, the --discard-untrimmed wouldn't work because the filtering was too restrictive or too lax, right? Or I am wrong?
I have found this post in the forum: some questions about cutadapt demux-paired - #3 by LiuZjiia
And it was really useful, I will add the extra-parameters you suggest! But I still has the filtering question in mind.
Again, thank you so much again for your help!!
Elsa