Identifying DMR

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.

Going forward

1. Write methods and results
2. Obtain other important methylation landscape information
3. Annotate DMR locations
4. Start RNA-Seq analysis
5. Create OSF repository for all intermediate files