Difference in GC content between samples

[iside]

Dear all,

I have a question about GC content in RNA seq. I know that it is not consistent between samples, and this is something to take into account while performing analyses. But why is there such a difference between samples?

I read through the literature, but the reason is still not clear to me.

Thanks for any suggestion.

[dpryan]

Generally there isn't much difference between samples, but if you run into this the typical reasons are:
1) Large numbers of differentially regulated genes, which will change the GC distribution of the resulting reads.
2) Different kits used for different samples.
3) Contamination in some samples.

Those are the sorts of common reasons you'll bump into, though there are likely many more.

[pmiguel]

I think rRNA often has a higher GC% than the rest of the transcriptome. You might want to check if that is the case in the organism you are working with and check if the % of ribosomal reads is higher in the samples where you observe aberrant GC%.

--
Phillip

[iside]

Thanks Philip,