Is it normal to obtain just a blue line in the "Per base sequence quality module" in FastQC (green background)?

I don't get any box plot. RNA-seq was carried out in Illumina NovaSeq6000. The sequencing reads were generated as paired-end data.

enter image description here

Regards, and thank you so much.

rna-seq fastqc

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updated 4.9 years ago by dariober

• written 4.9 years ago by sbruzual •

1 answer

Your data seems to be of very high quality so nothing to worry. You can extract the raw data used to generate this plot from the .zip file that accompanies the HTML file for this sample and plot the results out using a different Y scale.

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written 4.9 years ago by GenoMax

I think there is something odd. The blue line should be the mean quality and so it should be contained in the box & whiskers which are not visible. Maybe the OP should post more output from fastqc and together a bunch of reads.

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written 4.9 years ago by dariober

That is likely a quirk of plotting. Here is one recent 50 cycle NovaSeq run. enter image description here

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written 4.9 years ago by GenoMax

Wow! I was going to add to my comment above that such quality is too good to be true anyway - apparently it's not!

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written 4.9 years ago by dariober

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