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How to compute average methylation among multiple sites given raw sequencing reads
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Entering edit mode
5.4 years ago
zhourudy2 • 0
United States

I have a question regarding calculating average methylation across all sites from one single gene. I have the raw data from chip bis sequencing in the following form.

15, 5,0.33

20,5,0.4

10,5,05

My question is since the total number of reads at different sites is different, which would be a better way to compute average methylation?

1. Take the ratio and divide by number of site?

2. Take the sum of #of C reads among all sites/ sum of Total reads?

I am leaning towards method #2 since I feel like its a more accurate depiction of the raw data but I wanna hear some opinions!

Thanks!

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Entering edit mode

there is a typo - the second column should be 20,5,0.25

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Entering edit mode
15 months ago
Freiburg, Germany

It's probably best to just take the weighted average. So for this "gene", you'd get:

0.33*(15/(15+20+10)) + 0.4*(20/(15+20+10)) + 0.5*(10/(15+20+10))


which is ~0.399.

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Entering edit mode
16 months ago
feljpants • 0

the simple average and the weighted average output the same methylation percentage

18/45 = 0.33(15/(15+20+10)) + 0.4(20/(15+20+10)) + 0.5*(10/(15+20+10))