Question: What is the purpose of testing GC contents during a transcriptome sequence?
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gravatar for tingtingxu0411
14 months ago by
Beijing
tingtingxu04110 wrote:

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?

ADD COMMENTlink modified 14 months ago by lakhujanivijay4.8k • written 14 months ago by tingtingxu04110

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

ADD REPLYlink written 14 months ago by ATpoint31k
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gravatar for lakhujanivijay
14 months ago by
lakhujanivijay4.8k
India
lakhujanivijay4.8k wrote:

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.

enter image description here Source: fastqc module help

ADD COMMENTlink written 14 months ago by lakhujanivijay4.8k
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