---
title: "January 2024, Daily Log"
author: "Kathleen Durkin"
date: "2024-01-31"
categories: ["daily log"]
format:
  html:
    toc: true
---

## 31 January 2024

#### Wednesday

-   More debugging of *P.evermanni* RNAseq abundance quantification. (See [Github issues](https://github.com/RobertsLab/resources/issues/1793) and [notebook post](/posts/projects/E5_coral/2024_01_31_Peve_kallisto.qmd) for details)

## 30 January 2024

#### Tuesday

-   class/classwork (prep and leading FISH510 discussion)
-   Consolidated a bunch of cool ideas/questions fro future reading/projects [here](/posts/projects/misc/2024_01_30_Ideas.qmd), will make this my go-to document for recording this stuff (so I don't just forget it all!)
-   my fix for reformatting the converted gff -\> fasta file for P.evermani kallisto indexing is not working, due to a mysterious issue with fastx_collapser -- details in [github issue](https://github.com/RobertsLab/resources/issues/1793)
-   Finished running *P.meandrina* kallisto (code [here](https://github.com/urol-e5/deep-dive/blob/main/F-Pmea/code/14-Pmea-RNAseq-kallisto.md), output matrix [here](https://github.com/urol-e5/deep-dive/blob/main/F-Pmea/output/14-Pmea-RNAseq-kallisto/kallisto/kallisto.isoform.counts.matrix)).

## 29 January 2024

#### Monday

-   Class and classwork

-   P.evermanni kallisto work -- think I figured out how to convert gff to fasta and reformat appropriately for kallisto indexing (bedtools getFasta, fastx_toolkit fasta_formatter, fastx_toolkit fastx_collapser)

## 26 January 2024

#### Friday

## 25 January 2024

#### Thursday

Finished running *A.pulchra* kallisto (code [here](https://github.com/urol-e5/deep-dive/blob/main/D-Apul/code/14-Apul-RNAseq-kallisto.md), output matrix [here](https://github.com/urol-e5/deep-dive/blob/main/D-Apul/output/14-Apul-RNAseq-kallisto/kallisto/kallisto.isoform.counts.matrix)). I did see that there's already a count matrix for *A.pulchra* linked in the deep dive repo ([here](https://github.com/urol-e5/deep-dive/wiki/Expression-Data-Types)), but it's different to my kallisto output -- maybe run using different reference? Isn't entirely clear, but I think that may be from the lncRNA work, which was using genome reference through HiSat?

Also started on process for *P.evermanni*, but realized that reference data is only available as a CDS gff file, not as a FASTA, and kallisto requires FASTA format to generate an index. I think I'll ask about it at Science Hour tomorrow

## 24 January 2024

#### Wednesday

-   got going on A.pulchra gene expression work, working out kinks of finding/downloading trimmed RNAseq reads and appropriate transcripts reference, and running through kallisto

-   listened to this week's chapter for DEI meeting tomorrow

## 23 January 2024

#### Tuesday

-   class and classwork -- Megan and I are picking papers for our FISH510 meeting next week that's focused on epigenetics!

-   looked through [cod RNA extraction QC report](https://github.com/RobertsLab/project-cod-temperature/blob/main/data/Sample.QC.report.of_30-943133806_240118025106.xlsx) and revised selection of [samples for methylation](https://docs.google.com/spreadsheets/d/19CqqS3wOhmG7drw163v7evUylRWwOjBOdvuR-y0RqF0/edit#gid=155247170) work. Only tissue samples that a) are being RNAseq'd; b) have sufficient RNA quantity; and c) have RIN values \>6 were considered

## 22 January 2024

#### Monday

-   Finally got access to TREQ!

-   Classwork

-   finished high-level summary of smRNA ID workflow for E5 deep dive manuscript

-   Proposal writing class -- we watched an example of an animated video over-viewing a lab's work w/ microplastics in a very general-public-friendly way, it was sick! That would be a really cool component to create for the lab or for a future project/grant/proposal

## 19 January 2024

#### Friday

-   Read some papers for FISH510 -- one of them, Császár et al. 2010 (adaptive potential of a set of coral and symbiont stress response traits) got me wondering about what DGE analysis work has been done on the symbionts separately from the host?

-   Discussion write up for FISH510

-   prelim work on cod DGE paper

## 18 January 2024

#### Thursday

Lab meeting -- Chris made a really awesome, helpful comment about remembering to enjoy the process of work/grad school, and Grace mentioned she's using a new method to improve her productivity/focus by specifically allocating timed sections of work time and downtime (e.g. 25min working straight through, then 5 min for standing up, walking aruond, anything non-work related) that I think I'm going to try!

Ariana suggested assembling de novo transcriptome from our rnaseq data, which I know is a thing but I still don't really get it...? How can you get useful/trustworthy information by comparing your data to itsself...?

\^in effort to make sense of above question I made a quick sketch -- I think it's something like this? I realized that I forgot (for the nth time) that I'm working with RNA now, not DNA, so there are multiple copies of every sequenced transcript, and for DGE work the relative abundances of the transcripts, rather than presence/absence, is what matters.

![](/images/DGE_sketch.png){width="400"}

Feeling very dumb and confused about the minutia of how to do the deep dive gene expression stuff so switched back to a generic DGE pipeline in preparation for the cod samples. Going to use Megan's clam data (see full discussion of her work[here](https://faculty.washington.edu/sr320/posts/frontpage/megan-rna/)) as test data to push through my workflow.

## 17 January 2024

#### Wednesday

After talking w Zach I think I have an idea of how to start writing up a condensed version of the sRNA methods for the deep dive ncRNA manuscript.

Also, Zach and I talked about how to move forward with gene expression analysis for the E5 deep dive. We have trimmed RNAseq reads for the three species but we couldn't find any published transcriptomes. However, for P.meandrina we found NCBI published gff files with only annotated protein-coding genes, which could maybe be used to approximate a transcriptome file? We're not sure if that work correctly with kallisto though, or if we'd still need to use HiSat...

Read up on some of the sncRNA tools we used to write up on them in the deep dive manuscript (loving how it takes like 40min of reading to write 1 summary sentence of how something works).

## 16 January 2024

#### Tuesday

Continued compiling/modifying/writing code for a general RNAseq analysis pipeline for use in the cod and/or E5 projects. Will be meeting w/ Zach tomorrow to talk about E5 molecular stuff (writing and gene expression analysis)

Class

Did some work on updating CV

## 15 January 2024

#### Monday

Classwork + papers

## 12 January 2024

#### Friday

E5 Molecular group meeting (notes [here](https://docs.google.com/document/d/1IgbZgJOcZYKogHhHB1Apst1ihhXzmYLT-fLHrZf0dtc/edit?usp=sharing))

Classwork

## 11 January 2024

#### Thursday

eScience Institute Data Carpentry workshop, Day 4

## 10 January 2024

#### Wednesday

eScience Institute Data Carpentry workshop, Day 3

Finished [review of TTS tools](../../projects/misc/2024_01_02_TTS.qmd) -- I think I'm going to go with Speechify

## 09 January 2024

#### Tuesday

eScience Institute Data Carpentry workshop, Day 2

Classes, finished transcribing [SICB notes](../../projects/misc/2024_01_02_SICB.qmd)

## 08 January 2024

#### Monday

eScience Institute Data Carpentry workshop, Day 1

First day of classes for the Winter quarter

## 06 January 2024

#### Saturday

[SICB Day 5](../../projects/misc/2024_01_02_SICB.qmd#sicb-day-5)!

## 05 January 2024

#### Friday

[SICB Day 4](../../projects/misc/2024_01_02_SICB.qmd#sicb-day-4)!

[Cnidarian Social](../../projects/misc/2024_01_02_SICB.qmd#cnidarian-social) after the conference -- super fun!

Talked w Steven about next steps of coral stuff -- move towards combining sRNA and RNAseq stuff to examine how the sRNAs are involved in genome expression

## 04 January 2024

#### Thursday

[SICB Day 3](../../projects/misc/2024_01_02_SICB.qmd#sicb-day-3)!

## 03 January 2024

#### Wednesday

[SICB Day 2](../../projects/misc/2024_01_02_SICB.qmd#sicb-day-2)!

## 02 January 2024

#### Tuesday

[SICB Day 1](../../projects/misc/2024_01_02_SICB.qmd#sicb-day-1)!

-   MISS Grant Writing Workshop (notes [here](https://docs.google.com/document/d/1_OzDwwrB3_MgcHZMNjwzF8FmA6CmD3FxBc-V2bGYIhQ/edit))

-   MISS Figures and Illustrations Workshop

## 01 January 2024

#### Monday

-   Did some Lab Notebook work -- set up new section for miscellaneous posts, set some January goals, and set up my January daily post page (which you're currently reading)

-   Went through the (many, many) talks/events at SICB for the first few days and planned out my itinerary

-   Started writing up my review of different TTS services -- find details [here](../../projects/misc/2024_01_02_TTS.qmd)
