Tumbling Oysters

Categories

All (59)

GO (2)

Quarto (1)

R (13)

analysis (1)

annotation (1)

aquaculture (4)

bismark (2)

blast (6)

ceabigr (2)

cod (6)

code (2)

coral (1)

cron (1)

datasets (4)

deepdive (2)

e5 (10)

eDNA (1)

fish546 (1)

gene ontology (1)

ggplot (2)

hardening (1)

highlight (1)

hisat (3)

hpc (1)

hyak (1)

igv (1)

klone (2)

lncRNA (1)

lncRNA) (1)

lncrna (2)

log (1)

methylation (8)

methylkit (1)

mytilus (3)

news (6)

noteboook (3)

oyster (8)

paper (8)

qPCR (1)

rstudio (1)

rsync (1)

seastar (1)

snp (2)

stress (1)

temperature (2)

thoughts (1)

tidyverse (4)

xargs (1)

Megan it

eDNA

fish546

taxa id from seq reads

Energy Stating

e5

methylation

Can we predict where they are on the curve

Getting to GO with Phenotype

e5

GO

A short list for machine learning

OA OA OA

oyster

methylation

Bringing diploid - triploid to an end?

lncRNA Discovery Pipeline

e5

lncRNA)

This lab notebook documents the process of identifying long non-coding RNAs (lncRNAs) from RNA-seq data. The pipeline includes data acquisition, genome alignment, transcript…

Please Klone me

hyak

hpc

rstudio

Getting on the Rstudio Klone Machine

Apul Time Series Methylation

e5

methylation

coral

bismark

It’s in the name…

We wish you a Merry Mytilus!

mytilus

methylation

methylkit

Time-series Apul lncRNA count matrix

e5

lncRNA

and the path to get there

Mytilus DNA methylation calls

mytilus

methylation

bismark

associated with contaminants

Hip Hip Array

methylation

klone

Knocking out the code to get bismark happy

Running Bismark in SLURM Array for Methylation Analysis

methylation

klone

Stats on e5 genomes

e5

welcoming new pulcra

Connecting annotations

blast

hisat

annotation

challenges post HiSat

re prime

oyster

stress

Giving 10k seed more resiliency

R N A T O G O

blast

e5

On the Roan to assigning GO to genes

Git that Pro GO

blast

e5

Deep dive Protein Annotation

Double header

oyster

temperature

larvae, ploidy, and 10k seed start

Oyster bath

oyster

temperature

When is it too hot?

Huddl Launch

oyster

aquaculture

First of season day 3 larvae are a go!

Repro Repro

blast

gene ontology

Pipeline for Reproduction Annotation

Spring Cleaning

oyster

aquaculture

Getting ready for spawning

Seed travels

oyster

aquaculture

the Wescott Bay Deployment

HiSat that SeaStar

hisat

seastar

finally overcoming gtf h$11

xargs

xargs

now with no reason for loops

That escalated quickly

cron

rsync

log

going from 1 line script to cronning a sys log

Working with IGV

R

igv

cod

Getting appropriate IDs for Gene, Transcripts

R

blast

cod

for cod, looking ahead to Uniprot Accessions

Differentially Expressed Transcipts

R

datasets

cod

Differentially Expressed Genes

R

datasets

cod

Looking at Apul miRNA

R

datasets

cod

HiSat

R

hisat

Genome files

R

datasets

cod

Launching more stress

oyster

hardening

aquaculture

starting new seed and adult hardening

What I have been up to today

thoughts

February Daily

noteboook

Your text here…

Apul lncRNA Discovery

deepdive

R

lncrna

e5

Steven Roberts 03 November, 2023

November Daily

noteboook

Went to hatchery to clean oysters. A couple of pipes in control fell. Temperature was 13.9. Installed header heater to 16.

Correlating Matrices

ceabigr

R

tidyverse

methylation

snp

Steven Roberts 11 September, 2023

Peve lncRNA alignment

deepdive

R

lncrna

e5

Steven Roberts 08 September, 2023

Epidiverse GRM

ceabigr

R

tidyverse

ggplot

snp

re-evaluating the grm

Myt Iso-seq Annoation

mytilus

R

tidyverse

blast

GO

code: https://github.com/mattgeorgephd/PSMFC-mytilus-byssus-pilot/blob/main/code/06-annotation.Rmd

ggplotting some qPCR

Quarto

R

tidyverse

ggplot

qPCR

quick take on graphing out some of Noah’s data

Mytilus Iso-seq Data check

noteboook

Lets take look at Isoseq fasta

DNA Methylation and Species/Tissue Specific Considerations

news

Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases

Epigenetic mechanisms in marine invertebrates

paper

Trigg, S. A., Y. R. Venkataraman, M. R. Gavery, S. B. Roberts, D. Bhattacharya, A. Downey‐Wall, J. M. Eirin‐Lopez, K. M. Johnson, K. E. Lotterhos, J. B. Puritz, and H. M.…

Celeste Valdivia

DNA Methylation Analysis Methods

[]

Tutorial #5 Reflection

news

For the last week of our tutorial, we came back to DNA methylation and read another Roberts lab joint: https://doi.org/10.1111/1755-0998.13542

Grace Leuchtenberger

Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra

paper

Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra

The Role of DNA Methylation and Context Dependence

paper

Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates?

Molecular stress responses in marine intertebrates

paper

Roberts, S. B., and M. R. Gavery. 2012. Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates? Frontiers in Physiology 2. https://doi.org…

Celeste Valdivia

Tutorial #4: DNA Methylation Station

news

For our tutorial this week, I read the paper assigned to everyone, a Roberts lab special:

Grace Leuchtenberger

Molecular stress responses in marine intertebrates

paper

Two weeks ago members of our FISH 600 reading group were asked to select papers to present that cited the following paper:

Celeste Valdivia

DNA Methylation Synthesis

paper

ntic](“https://github.com/sr320/tumbling-oysters/blob/main/posts/ChrisPosts/epigenticPath.png?raw=true”) ---

New Family on the Block

Week 4 Reflection

paper

This week we read Gleason & Burton’s 2015 RNA-seq reveals regional differences in transcriptome response to heat stress in the marine snail Chlorostoma funebralis and found…

Tutorial #2 Reflection

news

Last week, almost all the papers we talked about looked at different living conditions for marine invertebrates and how that influences gene expression or gene regulation.…

Grace Leuchtenberger

Genetics: Does it really matter?

paper

highlight

code

Here I will describe a recent, cool paper and try to also highlight 1) some of the material covered in our class on Proposal Writing and Professional Development, and 2)…

Post With Code

news

code

analysis

This is a post with executable code.

Welcome To My Blog

news

This is the first post in a Quarto blog. Welcome!

Tristan O’Malley