I am starting my studies in Microbiome, so I don't have the experience to analyze my quality data from the forward and reverse sequences obtained after removing the primers.
As I received the files without the barcodes, I imported the paired-end-sequences to Qiime2, removed the primers using the command below (following the tutorials available), and proceeded with the quality demux of both sequences, as follows:
qiime cutadapt trim-paired
After removing the primers, I had a forward sequence of 237 bases and a reverse sequence of 275 bases, with an overlap of only 38 bases. Does anyone know if this is enough to continue the analyses? Also, the Q score varied over the sequence, mainly at the end of the reverse sequence, so I don't know how to proceed with the dada2 denoise-paired. Should I use both sequences or just one of them? Still, should I trim the sequences with low Q scores or not? My concern is related to the short size of the overlapping.
Can anyone help me, please?