Per base sequence content variation after doing fastqc
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?
1 answer
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.
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You should read https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/ and other related blog posts by authors of FastQC.