Last month I encountered more struggles with R and
methylKit than I anticipated…and did you know that not having DML is a bottleneck when you’re trying to understand methylation responses to ocean acidification?!??! Sigh. I made some progress that I think sets me up really well to finish my dissertation goals this month, so at least that’s good!
Hawaii Gigas Methylation:
- I extracted SNPs from bisulfite sequencing data with
BS-Snper! I have SNPs for each individual oyster, as well as SNPs from a merged BAM file. I didn’t get a chance to review SNP data or try
EpiDiverse/snpjust yet, but I have SNPs.
- I didn’t work on getting DML from
methylKitbecause I spent several weeks troubleshooting
methylKitwith the Manchester data. But, I have made progress on identifying a method!
- Decided not to get a WGS resequencing quote from Genewiz since we already have one from UW, and UW is likely cheaper!
Gigas Gonad Methylation:
- Extracted SNPs with
- Embarked on a SAGA to identify DML using
methylKit, which included testing the base code, separating female and indeterminate samples, preparing a
moxscript, running R on
moxin a SLURM script, calling an R script from a SLURM script, and finally, using the R Studio server. Now I have DML and a workflow!
- I paused work on the ocean acidification and reproduction review
AKA rolling over April Goals that were rolled over from March