Per base sequence content variation after doing fastqc

Question

[Luna]

I am doing RNA-Seq analysis and there is variation in %A and %T content and %G and %C content(per base sequence content) in the first few positions of the reads. The sequence quality scores are good (>30) for these positions. I was wondering if i should keep these reads for further processing or trim the first few bases which hava different base content and then continue my analysis?

[GenoMax]

You should read https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/ and other related blog posts by authors of FastQC.

Answer 1

[ATpoint]

Don't do anything, it's normal and expected, see for example How should I handle the raw reads with failed per base sequence content in fastQC and many other threads.

[Luna]

thank you!