'Perfect' RNA-seq base quality score

Question

[miller93]

Hi everyone,

I am new to RNA-seq and have I recently performed RNA-seq (Illumina NovaSeq 6000; 25M reads; PE, 100bp; Mus_musculus:mm10) on DA3 mouse leukaemia cells. I used FastQC to check the quality of my reads and was surprised by the high quality and lack of variability within the quality of the bases. The examples of base quality I have seen online all have variability, and the quality decreases toward the end of the read. I've linked an image of the Per base sequence quality.

https://freeimage.host/i/2UDpiQ

Any help or comments would be greatly appreciated.

Thanks in advance, David

[Ram]

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image or the HTML embed code, not the link to the webpage that has the image embedded (which is what you have used here)

Answer 1

[ATpoint]

Looks like just a normal sequencing runs these days, no magic here and nothing to worry about. In fact base quality is the most uninteresting in RNA-seq as it literally has no meaning unless it is a total catastrophe which these days is almost never.