GC bias between samples tolerance in RNAseq?
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4.1 years ago
annen ▴ 30

Does anyone have any info on the level of GC content disparity that is tolerable between samples? For example, if I have one group that has an average GC content of 41% (+/- 3) that I want to compare to one with an average GC content of 44% (+/- 2)- does this need to be accounted for in my analysis or is this considered equal? Any info is appreciated.

RNA-Seq GC bias • 1.9k views
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You've got bigger problems than GC content if you're trying to compare RNASeq between two different genomes. What is the experimental design?

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Sorry, I guess I was unclear. They are samples from the same species, just two groups- a control group and a treated group. If I look at the reads from the control group, they have a GC content of 44% (+/- 2) compared to my treated group that is 41% (+/- 3). Is this within tolerance for looking at differential expression between treated and control or something that I need to account for?

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That looks like a pretty big difference to me - which I wouldn't expect for a library between members of the same species. How many replicates do you have per group?

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That's what I thought... I have 5 replicates per group.

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Have you used the cqnplot() function from the cqn package? That'd be more useful than comparing averages.

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I have not.. I will try that and see what it looks like. Thanks.

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