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Identifying methylated CpGs in Cv gonad data #615

Closed yaaminiv closed 5 years ago

yaaminiv commented 5 years ago

I want to describe general methylation trends, irrespective of pCO2 treatment in my C. virginica gonad data. Claire and Mac both had sections in their papers where determined if a CpG locus was methylated or not. From Mac's 2013 PeerJ paper:

A CpG locus was considered methylated if at least half of the reads remained unconverted after bisulfite treatment.

I believe this was done methratio in BSMAP (Claire's notebook). Is there a way to do this with bismark or methylKit?

yaaminiv commented 5 years ago

I'd assume this would be the goal of unite in methylKit, but I haven't figured out why it's not giving us the output we want (yet).

sr320 commented 5 years ago

.cov files have methylation for each loci, as well as coverage.

Limit to 5x then you can call each loci. On Mar 17, 2019, 4:14 PM -0700, Yaamini Venkataraman notifications@github.com, wrote:

I'd assume this would be the goal of unite in methylKit, but I haven't figured out why it's not giving us the output we want (yet). — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

yaaminiv commented 5 years ago

To clarify: I plan on just looking at the 5 samples from the control to not induce treatment effects. Is this the correct approach?

sr320 commented 5 years ago

That is fine… On Mar 18, 2019, 9:04 AM -0700, Yaamini Venkataraman notifications@github.com, wrote:

To clarify: I plan on just looking at the 5 samples from the control to not induce treatment effects. Is this the correct approach? — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.