Checking for(a ton of) overrepresented sequences origins from 16S sequencing

Question

[regisantonioli]

Hello,

I am working with Illumina NGS 16S data, and I have run it through FastQC, but after checking the results I have over 600 overrepresented sequences. FastQC didn't identify any adapters or anything like that.

I'm aware that 16S data may have overrepresented due to it being the 16S amplicon sequences, and I am checking for it on Blast. My question here is that, since FastQC did not find any adapter, do I have to check each and every one of those 600 sequences on Blast? Or even if there is another more automated way to check for that. I'm rather new with this so I do not have much experience with how these things really work so I'm looking for someone to shed some light into this for me.

Appreciate the help!

Answer 1

[GenoMax]

I don't think so. "Failing" a test in FastQC does not mean you can't proceed with the rest of your data analysis. Use FastQC as a mile marker and not as a road block. If your results ultimately don't look reasonable then you can back track to find out what may be causing that problem.