Separate V1/V4/V6/V9 regions

Hi all,

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 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?

Best regards!

Sorry, but I really don’t understand what you’re asking. Here is a better worked example for how to generate a region specific reference. You shouldn’t use a fastq file to generate the reference…