Problem interpreting 'Per base sequence quality' report

Question

[Sanjukta]

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?

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

Answer 1

[Philipp Bayer]

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!

[Sanjukta]

Thanks a lot