Negligible methylation in mitochondrial sequence

[yaaminiv]

I created an IGV session to look at methylation in the mitochondrial sequence. This is the mitochondrial sequence I got from NCBI, not the separate sequence from the Roslin genome paper. The genome/index file I created with IGV can be found here

The mitochondrial sequence is predominantly unmethylated, but there are some methylated CpGs. Is this a sign that something when wrong in the alignment process?

[sr320]

What is the coverage threshold here?

[yaaminiv]

These are bedgraphs from bismark, no coverage threshold

[kubu4]

Also, make sure you're not viewing the mean values (IGV enables the mean view sometimes).

[yaaminiv]

Also, make sure you're not viewing the mean values (IGV enables the mean view sometime

Shoot good point. Here's the same region with no windowing function:

[sr320]

I would set threshold at 5x, and look again.

[yaaminiv]

I used 5x bedgraphs. Definitely better, but there are still traces of methylation

Full mitochondrial sequence:

Area 1:

Area 2:

How should I proceed? I could remove these locations from my dataset, try increasing coverage to 10x to see if they're still there, or re-map to the Roslin mitochondrial sequence.

[yaaminiv]

Good to keep moving forward

At some point, should check bisulfite conversion efficiency with spike in/mitochondrial methylation rate