Differential methylation analysis of low pH vs ambient conditioned geoduck hemolymph
- got methylkit running on Emu
- would be nice to have some genome annotations to see where exactly the differential methylation is
- from the results, maybe I can blast the regions and see where they map in other species?
- got methylpy running on Ostrich. It’s erroring out because something isn’t indexed and it’s not creating a bai file which it needs to.
- trying to run it on sorted bams to see if that helps
- try removing sample specific patterns by excluding the 284 temp affected proteins identified by clustering, ASCA, and proportions test
- didn’t make a difference, heatmap still shows sample specific patterns as opposed to commonalities between same-day samples
ASCA is helpful in identifying proteins affected by time
- leaving day 0 in is nice because it’s a good contrast to day 3. You can also really see the progression of development driven by temperature.
- these developmental proteins should be removed when thinking about just temperature effect; in other words to consider temperature specific effects that aren’t dependent on time, i think i need to remove some protiens that show significant effects from both and from the interaction and look at what proteins remain.
- maybe plot heatmap of proteins detected as time effected, temp effected, and interaction effected, and overlapping, see how these cluster on a heatmap.
- this way I can say what is development and what is temp effected non-dev. process i.e. infection