Looked at the combined Day 10 and Day 135 samples, with the inclusion of a time covariate.
These are the day 145 runs, with the corrected methylation cutoff logic. Macau was run outside of R-studio, to facilitate running multiple instances concurrently.
So I noticed that I was inadvertently trimming all methylation counts less than 10, as well as the total counts. I should not have done that. The good news is this nets us 267 DMRs as opposed to 41! The bad news, for some reason it makes MACAU run glacially slow.
Pseudocode description on how to combine multiple SNP files in to a single merged file, and then generate a relatedness matrix.
Running Methyl Extract on a single sample .sam file at a time.
Rough protocol outline after meeting with Micah at DNR in Olympia.
CpG O/E plot for Geoduck transcriptome, try 2.
Forest Plot code for Geoduck transcriptome methylation
Testing R notebook functionality with some Methylkit output from Steven's Oly samples.