May 10, 2019 WGBS Geoduck Hemolymph and Oyster seed proteomics

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