How the Exons, Introns and Intergenic proportions are calculated?

[j...@sanger.ac.uk]

Dear Konstantin,

Thanks for your effort with Qualimap. Is very useful!

I know this has been discussed in the past, but is not clear for me how this is working. 

I'm wondering if the issue with the proportion of reads mapping to exons, introns and Intergenic was solved in the new version of Qualimap (v2.2).

I have ran the RNA-seq QC and after adding, subtracting and dividing basically everything reported in the file, I didn't manage to figure out how the proportions are calculated or I'm missing something there. 

Here is enclosed a couple of examples. 

Any help will be great!

Thanks!!

[Konstantin Okonechnikov]

Hi Javier,

sorry for delay in reply, I missed your message previously.

The explanation for percentage is the following: the proportion of mapped reads is separated into exonic and intronic/intergenic

Total percentage is computed based on the sum of these reads.

So, in your case this will be:

49814794 + 9594474 + 1314923 = 60724191 (total)

Therefore, exonic percentage for example :

(9814794 / 60724191) * 100 = 0.820345

Note that intronic/intergenic overlapping exons is a portion belonging to intronic and intergenic, additional separate analysis.

The reads that do not pass correct counting approach are considered ambigious. 

Let me know if you have any additional questions,

   

   Konstantin

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[Javier Gutierrez-Achury]

Dear Konstantin, 

Thanks for your answer. 

Yes, this explains the percentages reported. 

I was confused due to other posts (about the same issue), where "Missing chromosome annotation" and "Not Aligned reads" were included in the percentage calculations. 

Best, 

Javier 

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