Genome DMR analysis
-
Re-called methylated cytosines with MAPQ score >= 20 using this script: 20190925_DMRfindDay10EPIsamples.sh
- allc files are here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20190925/
- NOTE: these are not destranded. I attempted to make destranded allc files in the same script but something happened (gzip: stdin: unexpected end of file). I still need to debug this.
- Reran DMRfind on new allc files with this script: 20190926_DMRfind3clstAllEPIsamples.sh
- This required 3 individuals/group have coverage of the DMR
- DMR output files are here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20190926/
- Plotted DMRs as heatmaps
- next steps:
- functional annotation