I have 16s data the attached is the QC report shows some errors should I need to remove overrepresented sequences? I did it using fast P but keeping the default parameter P=20 but it did not make any change to the report.
Are you sure you want to remove the overrepresented sequences? Sometimes, these are the differentially expressed transcripts you're looking for across conditions, and so you wouldn't want to remove them. Because they do not seem to come from adapters, I think leaving them is fine.
If you do want to remove them, I'm not sure how to answer your question, but I know other users will ask you to provide the code you used, so you should start with that.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
Daniel, I appreciate your comment. I'll leave it as is, but after reading this report, is there anything else that needs to be improved upon?
Well I can only see what passed or failed, but I would double-check GC content and make sure you know why it failed (maybe the reason is ignorable).
I'm pretty new at this myself, so my biggest advice is to use online guide's and manuals to see if you feel confident in your results. Here's an example: https://dnacore.missouri.edu/PDF/FastQC_Manual.pdf
I came to realize that there is usually not a clear-cut "pass" or "fail" when it comes to fastqc, rather it is a holistic overview of how "okay" your data looks. So I would go through the tutorials, see how your data matches and doesn't match, and if it doesn't match, try to google why.
Sounds great! I'll check that Thank you so much for your input.