What is the purpose of testing GC contents during a transcriptome sequence?

Question

[tingtingxu0411]

What is the purpose of testing GC contents during a transcriptome sequence? What is the value of GC contents generally? What is the meaning of high GC contents?

[ATpoint]

There is a nice video from Mike Love on the matter, see here.

Answer 1

[lakhujanivijay]

In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

Source: fastqc module help