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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]

Tues. Sept 25, 2018

My goals for today Get personal items from Mukilteo field station done Farewell lunch at noon done Get everyone’s thoughts on water chemistry data table for crab metabolomics paper done [Read More]

Mon. Sept 24, 2018

My goals for today Lab meeting @ 10 Meet with Steven to decide projects to focus on SAFS kickoff @ 2-5 Notes from lab meeting Sam’s working on oyster transcriptome and genome assembly Kaitlyn’s working on oyster proteomics temperature x time series analysis pharmacokinetics toolkit applicable? (Brent asked) RNA-seq time... [Read More]