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Tues. Oct 9, 2018

ASCA analysis with oyster proteomics temperature x time series dataset Goal: To determine if proteins drive difference between temperature groups over time we need to understand the model that ASCA creates from the data so we want to extract the loadings from the temperature factor ASCA and try to understand... [Read More]

Mon. Oct 1, 2018

My goals today Get Husky card Get bus pass Geoduck meeting @ 1:30p notes from meeting: How frequently to sample Why are animals limited to 80? because feeding of live algae is limiting benefits of live algae vs. paste paste better because doesn’t mess with pH and we can have... [Read More]

Friday. Sept 28, 2018

##My goals for today work on Bismark alignment comparison how does Bismark compare to Methylpy? reference papers: jupyter notebook install methylpy try bowtie vs. minimap make genomes Insert size alignment setting in bowtie, this is the -I parameter default is 0; in methylpy it’s 20. Roberto’s last day lunch @12:30... [Read More]

Thurs. Sept 27, 2018

My goals for today FISH 546 9-10 Epigenetics reading group @ NOAA NWFSC 12:30-1:30 transgenerational of envronmental info thoughts: stress opens heterochromatin => transposon/pseudo gene?/protogene? expression; does the cell just go crazy under stress and hope something works? Or is there a non-random mechanism that selects for advantageous changes? siRNAs... [Read More]

Wed. Sept 26, 2018

My goals for today Work on Bismark alignments Trying different alignment score settings: Looked into bowtie2 alignment manual alignement score is dependent on matches and mismatches alignment score of 0 = 100% perfect match 1 mismatch = -6 score 1 ambinguous character = 1 if there’s a gap in the... [Read More]