More RADMeth strangeness:
I finished the Day 135 samples in methcounts and ran them through the RADMeth program a few different ways. First (not really, it just happened to be faster) I looked at DMRs in Low vs Super Low pH treatments. The results were… even stranger than yesterday’s for Day 10 stuff.
That’s the one DMR between the two samples. With… 0 methylation in all samples? I read a ton of messages on the methpipe boards and no one has encountered a similar experience, but it looked like most of them were doing mouse/human stuff with super robust genomes to reference, so maybe that’s our issue? Something like RADMeth assuming chromosomes in the genome and maybe large swaths of methylation to compare against. Just an idea? Still trying to figure out how to look at/display the pre-merged DML data from RADMeth.
I also looked at hypomethylation in the Day135 samples. Bed and IGV XML files are found here.
Might be some interesting results here, I’m working on a good way to compare Day10 and Day135 samples, Maybe just by scaffold, since in all likelihood there won’t be overlap reliable.
Will update this with the R notebook once the Day 135 Ambient/Non-Ambient samples are finished running in RADMeth.