I am interested in separate 4 hypervariable regions of 16S ribosomal gene from a unique fastq file. I have all primer sequences for each region without barcodes. I used the pcr.seqs for extract each region but was discarded many sequences.
I am also trying to construct a database of each region(v1,v4,v6 and v9) according to this https://github.com/mothur/mothur/issues/235. I am trying to align this against my fastq file, but I am confused as extract my reads after the alingment. How can I do this? Is there a better approach?