Question

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

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2.6 years ago

sbruzual • 0

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 • 1.3k views

ADD COMMENT • link updated 2.6 years ago by dariober 14k • written 2.6 years ago by sbruzual • 0

score 0 · Answer 1 · 2021-09-22

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2.6 years ago

GenoMax 141k

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.

ADD COMMENT • link 2.6 years ago by GenoMax 141k

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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.

ADD REPLY • link 2.6 years ago by dariober 14k

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

ADD REPLY • link 2.6 years ago by GenoMax 141k

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

ADD REPLY • link 2.6 years ago by dariober 14k