How to deal with the error for "Per Sequence GC Content" in FastQC tool?

Question

[Researcher]

I am working on the genomic data of E. Coli. My sequence reads are of high quality, and I already removed the adaptors and overrepresented sequences. However, for all of my samples, I received a warning for "Per Sequence GC Content" in the FastQC tool, and for a few of my samples (around 2% of my samples), I received an error in this field. How should I deal with that? Should I remove the samples which have an error for "Per Sequence GC Content in FastQC"?

[shell241]

I have the same question with you. How did you finally solve the problem?

[GenoMax]

This is not a problem in many cases. Did you read the blogs I linked below? Otherwise show us a screenshot of the plot in question.

Answer 1

[GenoMax]

Warning/Error in FastQC need to be taken with a grain of salt and keeping the context of experiment you are doing in mind. They are rarely show stoppers. Post screenshots of what you are referring to using these instructions: How to add images to a Biostars post

Take a look at number of informative blog posts by FastQC authors that you will find of interest.