I'm doing RNA seq but the quality control sequence GC contens shape looks weird...

Question

[Kaia]

It looks like trident like Ariel's father using... I'm curious why this shape is so weired. Now I'm analyze 22 samples but, all of them look like this. Is it okay keep going analyze?,,,

Answer 1

[GenoMax]

It is not always possible to provide a logical explanation for things you see in FastQC since the results are a summary plot of millions of reads. FastQC is a QC tool and nothing prevents you from moving on with your analysis. If you notice specific problems downstream then you can backtrack and try to find a cause.

[jared.andrews07]

This is particularly true for RNA-seq data. Some very highly expressed genes have more/less GC than your average gene, which contributes to these sorts of peaks and valleys. As GenoMax stated, nothing to worry about unless things downstream look very wrong.