I’ve been working on Hollie’s Geoduck samples for a while now, and I have some results! Sort of… This is for 4 of the 53 samples, but it serves as a proof of concept for the workflow if nothing else!
Some pictures of what things need to look like.
Predictor file:
Relatedness file: (Note, Our relatedness values look wonky because there are only 4 samples in the group, and VCFtools calculates expected values directly from the samples)
The above two have no headers or row IDs, and are put in in the same order of sample columns from the Methylation and Total Coverage files.
Methylation Count File:
Total Coverage Count File:
Feed all of that in to MACAU and you get to see this!
which eventually spits out some results.
Results can be found here
Will follow this with an R notebook of what I did to make the total methylation and total coverage count files shortly.