About per tile sequence quality

Question

[Chris]

Hi all, I check a pair-end read sample and got this per tile sequence quality. Should I accept this sample? Thank you so much :) .

I read this but not sure if accept the warning and failure in this case. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/12%20Per%20Tile%20Sequence%20Quality.html

Answer 1

[GenoMax]

This should be fine. While one would want a pristine image (which is synthetic btw) this should not cause issues with your data analysis.

If your plot had looked like what is shown in the link you post above then it would be a cause to worry.

[Chris]

Thanks Max for your help. Would you explain a little bit about the number on the y-axis? So one or two red tiles are still fine.

[GenoMax]

Number on Y axis are tile names that indicate the surface of the flowcell (top/bottom), swath, actual tile number. These vary with type of flowcell (e.g. for NovaSeq 6000 see page 73 in this document).