Per tail sequence quality fail

Question

[misterie]

Hi again!

I have another problem with my data. FastQC returns red flag in per tile sequence quality. I see that this problem is often associated with reverse read of sequencing (in few lines). That data are representing WGS.

In other files I see horizontal red line through one tile.

What can I do with it? Should I remove bad tile or what? Thank you for your advices. I attached printscreen from my fastqc.

Answer 1

[Devon Ryan]

In your example there was a problem visualizing one edge of the flow cell (on both the top and the bottom of the flow cell). I suspect that the camera had problems.

There's nothing that you need to do on the bioinformatics side. Reads arising from those tiles will have lower quality and align more poorly...but that means they'll just get trimmed and filtered more, which is fine. If this continues to occur on this machine then you should contact Illumina, perhaps the camera needs a bit of servicing.

[misterie]

Ok. Thank you so much! So program for alignment can handle with it?

I thought that I need to do TILE FILTERING using FilterByTile.sh software. So that step is unnecessary? I can normally do alignment with this tiles problem?

[misterie]

I have presented graph after trimming (using trimmomatic). Does it means, that aligner (such as BWA) can handle with this tiles problem?