Primer removal in amplicon sequencing

Question

[sxf520]

Hello,

I am currently working with 16s and ITS amplicon sequencing data. I am processing this following DADA2 pipeline. I got the primer sequence for 16S as:

16S Amplicon PCR Forward Primer = 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG

16S Amplicon PCR Reverse Primer = 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC

I think these have the overhang portion with the gene specific part. When I search for primers should I input the whole sequence or just the gene specific part? Because for full sequence search I get no primer hit, but for gene specific part I do get primer hits. Thanks!

[GenoMax]

If you are looking to remove the primer sequences then you can provide these to scan/trim programs like bbduk.sh from BBMap suite or fastp. They should be able to find parts of sequence that are present in your reads. Depending on where the sequence is you can ask the trimmer to remove the relevant match.

[sxf520]

Thanks. I actually want to know if I should use the full sequence (with the overhang part) or only the gene specific part as the primer sequene.

[GenoMax]

DADA2 pipeline states that all non-biological nucleotides need to be removed so choose accordingly: https://benjjneb.github.io/dada2/tutorial.html