How to handle "perbase quality failed" issue?

Question

[mathavanbioinfo]

Hi I have performed RNA fastqc analysis, the resulting plot attached here please share your idea how to handle "perbase quality failed" issue https://ibb.co/yS52BXp

Answer 1

[Papyrus]

For the 5' bias in base content: check this answer and the blog post linked to there.

Additionally to the 5' bias, you can see 3' bias in base content. If this bias is gradual I'd say adapter contamination and you should trim your data. In this case the bias is abrupt and pertains to the last base. This could be observed if your data are already trimmed? When you trim adapters with high stringency, all the reads ending in the first base of the adapter (e.g. "A") will have that base removed, therefore none will end in "A".

[ATpoint]

Agreed, please just google "RNA-seq per-base fastqc biostars", you will find plenty of threads. Bottom-line: Ignore it and proceed with downstream analysis.