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Identifying methylated CpGs in Cv gonad data #615
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I'd assume this would be the goal of |
.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 ***@***.***>, 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).
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To clarify: I plan on just looking at the 5 samples from the control to not induce treatment effects. Is this the correct approach? |
That is fine…
…On Mar 18, 2019, 9:04 AM -0700, Yaamini Venkataraman ***@***.***>, 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?
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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:
I believe this was done
methratio
in BSMAP (Claire's notebook). Is there a way to do this withbismark
ormethylKit
?The text was updated successfully, but these errors were encountered: