Killifish Hypoxia RRBS Part 12
Penultimate step for methylation analysis: DMR identification! I ran the following code interactively to make sure I could call DMR and wouldn’t run into another error.
BAT_DMRcalling \ -q /yaaminiv/killifish-hypoxia-RRBS/output/05-analysis/summarize/all_pop/all_pop_metilene_N_S.txt \ -o /scratch/06-DMR/all_pop \ -a N \ -b S
I still got 0 DMR, but I had slightly more confidence in it knowing that the output files from
BAT_summarize went through
BAT_overview well. I created a script for
BAT_DMRcalling, environmental variable file, and SLURM script.
My confidence was short-lived…because every single one of my contrasts yielded 0 DMR. This struck me as weird, but potentially related to the poor hierarchical clustering I saw. Even with bad hierarchical clustering,
methylKit is able to pull out DML, so maybe there’s some other setting that needs to be adjusted? I emailed Neel with my questions.
- Write methods and results
- Obtain other important methylation landscape information
- Annotate DMR locations
- Start RNA-Seq analysis
- Create OSF repository for all intermediate files