Fix per tile sequence quality?

Question

[serpalma.v]

I see the following FastQC results in the "Per tile sequence quality" module:

https://ibb.co/he9DBd

Compared to other threads and articles I have seen, this does not look so bad in comparisson, but I am not sure if I should try to fix it anyway, files have been already run through Trimmomatic for quality trimming and adapter removal.

Samples come from a Hiseq4000 machine.

Libraries were prepared using TruSeq Nano chemestry.

• Could you give me some advise on how to proceed with these samples?

• Also, I cannot get the y-axis: according to Illumina, there are 896 tiles in a flow cell. Are tiles binned (or skipped) by FastQC?

I appreaciate your contributions

Cheers!

Answer 1

[GenoMax]

I suggest that you don't doing anything for now. Go ahead and proceed with the rest of your analysis. Tiles are not binned by FastQC, sequencing cycles are.

[serpalma.v]

Thanks, do you have an idea why are there so much less tiles in the y-axis than tiles in the flow cell?