RSeQC geneBody_coverage and RPKM_saturation result exlaination

Question

[Hughie]

Hello!

Recently I'm doing post mapping quality check using RSeQC. I mainly checked geneBody_coverage and RPKM_saturation using its python module, but I don't know what's good and bad result, so I post my result here and wish your help.

I can't explain the result, I guess it's because of the degradation during polyA extration.

I see four graphs in this picture, I don't know how to judge the result through y-axis.

Thanks a lot for your help!!!

Answer 1

[gmacnunn]

To me it looks like a lot of 3' bias in your genebody coverage. This generally suggests that there is a significant amount of degradation in the RNA sample. The degradation is most likely to have occurred during the collection of the RNA. Check out the RSeQC vignette to see intact vs degraded RNA. Look up 3' bias in RNA seq to see what causes this. Sorry to bring the bad news.

I am less aware of the RPKM module