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Problem interpreting 'Per base sequence quality' report

I am trying to analyse RNA-Seq data on Galaxy. On performing FASTQC before and after trimming with Trimmomatic, my Per base sequence quality report looks link this. What is the interpretation? Can i move forward to the next step? Or this dataset has to be discarded?

enter image description here

Link to the complete reports of the same dataset file, before and after trimming. https://drive.google.com/drive/folders/1BGYwjNCrowIKuhcjhp4yklp1Sgly0j__?usp=sharing

galaxy fastqc
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written by Sanjukta • Sanjukta

1 answer

The blue line is the mean quality score which is very good, always around 36. See here for an example report of good sequences that additionally have boxplots: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/good_sequence_short_fastqc.html

Normally you have boxplots, I found an explanation for why your boxplots are missing in the Github issues: if the range is narrow no boxes are drawn. So your data is consistently too good :)

This run looks great to me!

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written by Philipp Bayer Philipp Bayer

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