Fix per tile sequence quality?
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4.4 years ago
serpalma.v ▴ 70

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!

fastqc DNAseq illumina quality control • 3.1k views
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4.4 years ago
GenoMax 123k

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.

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

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