Question: How to compute average methylation among multiple sites given raw sequencing reads
0
gravatar for zhourudy2
4.3 years ago by
zhourudy20
United States
zhourudy20 wrote:

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.

Total reads, # of C reads, ratio

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!

 

methylation chip-seq R • 1.4k views
ADD COMMENTlink modified 11 weeks ago by feljpants0 • written 4.3 years ago by zhourudy20

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

ADD REPLYlink written 11 weeks ago by feljpants0
1
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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.

ADD COMMENTlink written 4.3 years ago by Devon Ryan91k
0
gravatar for feljpants
11 weeks ago by
feljpants0
feljpants0 wrote:

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))

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by feljpants0
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