Let me put you in the picture: I have started to work with qiime2 (version 2.4) a month ago. With respect to my data is a 16S paired-end sequences (obtained by Illumina sequencing) and I have to determine the taxonomy and the microbiota diversity in the different samples. However, in this moment, I am struggling with the denoised phase.
Even when I have read cutadapt documentation as well as dada2 documentation, I still have some dudes about:
q2-dada2plugin, there is a parameter
--p-trim, which is useful to eliminate base pairs of the 5' end.
q2-cutadaptexits the command
trim-single(the firts one is for paired end sequences and the other is for single-end sequences). Thanks to this command, you can remove the primers in your data.
So, my question is: if you can use directly the
q2-dada2 to remove the primers base pairs, why in most of the papers suggest you use cutadapt before denoising?
I mean, the
q2-cutadapt trim option requires the primer set sequences and this reduce the error. But, if you can remove them at the same time of the denoising...
Also, I know cutadapt let you working with specific hypervariable regions of the 16S rRNA bacterial gen (for example). So, if you only work with one region it is not indispensable to use cutadapt, right?
Perhaps there are some technical specifications that I have overlooked or am unaware of?
Thanks in advance!!