FastQC's report -- 'Per base sequence content' heading odd wave

Question

[Hughie]

Hello!

I'm a beginner of bioinformatics and recently I got some FastQC report when QC my RNA-seq data, but I can't understand the odd situations showing below.

https://ibb.co/caxZEv

https://ibb.co/hU7ZEv

https://ibb.co/cnSZEv

I want to know what caused the heading odd waves and how to handle then during later analysis, do I need to trim the head?

Thanks a lot for your kindly answer and advice!

[cpad0112]

It seems to be adapter contamination to me.

Answer 1

[GenoMax]

Do not trim "head" of the reads .. unless these are known to be some sort of inline barcodes.
@James has already referred to the possible cause where we see this pattern. See this post for additional information.

[Hughie]

Thank you genomax! You are always so kindly! The additional information is so useful, Thank you again.

Answer 2

[James Ashmore]

If you're referring to the per base sequence content of the first 10 bases. This looks like insertion bias from the Nextera kit used to prepare sequencing libraries. Do you know what kit was used for sequencing? If it was a Nextera kit, you only need to worry about removing Nextera adapters.

[lelle]

I don't know... The second and third graph look a bit too strongly biased to be "just" nextera bias, in my opinion. Hard to say without further information on the library...

[Hughie]

Thank you lelle! So do you think it's necessary to trim the header 10 bases?

[lelle]

I think you need to find out what causes the bias. If it is Nextera bias, I agree with James, that you should not trim them. If it is something else, like a primer sequence, it might be advisable to remove it...

[Hughie]

Thank you James! I will check the kit and find out the reason.