September 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

1. Submit molecular underpinnings (Ch.1) to BioRXiv by end of month
2. A.pul gametogenesis multivariate analysis
3. Marine heatwaves manuscript functional annotation for DEGs
4. Full dissertation draft

Data analysis

1. Multivariate analyses for Ch2
2. Ch3 functional annotation and final cross-generational analysis

Daily log

September 2

• Off for holiday

September 3

• Sent 28 corals to Arizona from CBLS wetlab aquaria
• Sent Neptune Systems Apex units for repair
• Ch1 edits and updates

September 4

• Ch1 target gene list methods and compilation
• Ch2 holobiont protein QC and updates
• Ch3 func annotation
• Nyssa Meeting
• Grading TA meeting

September 5

• Ch1 target gene list compilation
• Ch3 reproductive responses genotype contributions
• Grading TA meeting

September 6

• Ch1 target gene list compilation
• Ch3 reproductive responses genotype contributions
• Grading TA

September 9

• Ch1 target gene list compilation
• Ch3 functional annotation workflow
• Ch3 results and methods section
• Updated Gen5 lab software to version 3.16 and downloaded data for Nyssa
• Lab storage inventory work

September 10

• Ch1 target gene list finished!
• Ch3 functional annotation workflow
• Ch3 introduction edits
• Ariana writing meeting

September 11

• Writing accountability - virtual
• Ch1 target gene list updates to results and discussion
• Ch3 functional annotation workflow - trinotate tmhmv2 module issues
• Ch3 introduction edits complete
• Ch3 update methods and discussion outline

September 12

• Ch3 genome RNAseq workflow write up (mapping most recent A.pul to genome assembly)
• Ch3 functional annotation workflow - trinotate signalp6 module issues
• Ch3 revisit discussion outline - lit review
• Ch1 edits to results and discussion
• Flo writing meeting

September 13

• BES writing accountability meeting - ch3 discussion paragraphs 1 and 2 - ch1 final results and discussion edits, sent to Hollie
• Ch3 functional annotation workflow - trinotate signalp6 module issues
• Ch3 revisit discussion outline - lit review
• Ch1 submit to Hollie
• Ch3 made mapping workflow to A.pul genome
• Ch3 literature review on gene expression carryover/heritability analyses
• Ch3 update results section
• Ch3 lit review on Fst and kinship coefficient analyses
• IDP completion

September 15

• Ch3 discussion paragraphs 1 and 2
• Ch3 Fst workflow for transcriptome variant calling
• DEIJ bullet points for Putnam Lab meeting
• Ch3 genotypic contribution model creation
• Ch3 hisat2 alignment to A.pul genome workflow

September 16

• Ch3 discussion paragraphs 1 and 2 edits
• Ch3 Fst workflow for transcriptome variant calling
• Running into length errors, I think this is due to transcripts compared to genes due to isoforms
• Putnam Lab meeting
• Ch3 genotypic contribution paragraph

September 17

• Ch3 discussion paragraphs 1 and 2 and 3 edits
• Ch3 Fst workflow for transcriptome variant calling using supertranscripts and trinity pipeline for GATK, etc.
• Jacob meeting
• Ch3 genotypic contribution paragraph and analyses for fertilization success
• Literature review for ordinal logistic regression model with temporal autocorrelation

September 18

• Ch3 intro and discussion edits
• Ch3 fst pipeline move all materials to unity through globus connect, not enough RAM on Andromeda
• Ch2 multicollinearity script and logistic regression
• Ch3 funtional annotation
• BES writing accountability Ch3 discussion paragraph 3 + 4

September 19

• Lab writing meeting, ch1 edits and feedback for ncRNA Jill manuscript
• Hollie meeting, ch2 and ch3 ways forward for story
• Ch1 edits
• Ch3 intro and discussion edits
• TA test prep for two sections

September 20

• Ch3 final func annot done
• Ch3 variant calling on globus connect and unity
• E5 molecular meeting

September 21

• Ch3 final func annot done
• Ch3 venn diagram for DEGs comparison
• Ch3 functional annotation goMWU methods and script

September 23

• Ch2 paragraphs 1 and 2 and abstract and intro edits
• TA grading
• Ch2 multicollinearity analysis
• Lab meeting

September 24

• Ch2 ordinal logistic regression analysis
• Ch3 discussion paragraph edits and paragraph three
• Ch3 func annot goMWU scripts
• Ch2 discussion paragraph 1 and 2

September 25

• BES writing accountability
• Ch3 variant calling script finished!
• Ch3 discussion paragraph three
• Ch3 introduction edits
• Ch2 discussion paragraph 3, introduction edits

September 26

• Ch3 vcf tools vcf concat
• Ch3 discussion paragraph 4 + 5
• Ch2 discussion paragraph 3, introduction edits
• Ch2 multivariate stats analysis

September 27

• Ch3 vcf tools vcf concat working throuh
• Ch3 discussion paragraph 6, intro add paragraph for energy trade off
• Ch2 discussion paragraph 4
• Ch2 multivariate stats analysis
• Ch3 larval daily measurements
• BES writing accountability