My Lab Notebook

##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]

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]

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]

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]

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]