R N A T O G O – Tumbling Oysters

Author

Affiliation

Steven Roberts

Professor, UW - School of Aquatic and Fishery Sciences

Published

August 27, 2024

tldr:

GO annotations for Deep Dive Transcript sets:

https://github.com/urol-e5/deep-dive/blob/main/D-Apul/output/20-Apul-gene-annotation/Apul-rna-GO.tsv

https://github.com/urol-e5/deep-dive/blob/main/E-Peve/output/20-Peve-gene-annotation/Peve-rna-GO.tsv

https://github.com/urol-e5/deep-dive/blob/main/F-Pmea/output/20-Pmea-gene-annotation/Pmea-rna-GO.tsv

This was done just as with proteins set (except different query and blastx as opposed to blastp)

Note both Proteins and transcripts wre obtained from: https://github.com/urol-e5/deep-dive/wiki/Species-Characteristics-and-Genomic-Resources

Actual code at

https://github.com/urol-e5/deep-dive/blob/main/D-Apul/code/20-Apul-gene-annotation.Rmd

https://github.com/urol-e5/deep-dive/blob/main/E-Peve/code/20-Peve-gene-annotation.Rmd

https://github.com/urol-e5/deep-dive/blob/main/F-Pmea/code/20-Pmea-gene-annotation.Rmd

---
title: "R N A T O G O"
description: "On the Roan to assigning GO to genes"
categories: [blast, e5]
#citation: 
date: 08-27-2024
image: http://gannet.fish.washington.edu/seashell/snaps/Monosnap_deep-dive__RStudio_Server_2024-08-27_16-05-41.png # finding a good image

author:
  - name: Steven Roberts
    url: 
    orcid: 0000-0001-8302-1138
    affiliation: Professor, UW - School of Aquatic and Fishery Sciences
    affiliation-url: https://robertslab.info
  #url:  # self-defined
draft: false # setting this to `true` will prevent your post from appearing on your listing page until you're ready!
format:
  html:
    code-fold: FALSE
    code-tools: true
    code-copy: true
    highlight-style: github
    code-overflow: wrap
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center", # Align plots to the center
  comment = ""         # Prevents appending '##' to beginning of lines in code analyses
)
```

tldr:

GO annotations for Deep Dive Transcript sets:

<https://github.com/urol-e5/deep-dive/blob/main/D-Apul/output/20-Apul-gene-annotation/Apul-rna-GO.tsv>

<https://github.com/urol-e5/deep-dive/blob/main/E-Peve/output/20-Peve-gene-annotation/Peve-rna-GO.tsv>

<https://github.com/urol-e5/deep-dive/blob/main/F-Pmea/output/20-Pmea-gene-annotation/Pmea-rna-GO.tsv>

------------------------------------------------------------------------

This was done just as with [proteins set](https://sr320.github.io/tumbling-oysters/posts/sr320-27-go/) (except different query and blastx as opposed to blastp)

Note both Proteins and transcripts wre obtained from: 
<https://github.com/urol-e5/deep-dive/wiki/Species-Characteristics-and-Genomic-Resources>

------------------------------------------------------------------------

Actual code at

<https://github.com/urol-e5/deep-dive/blob/main/D-Apul/code/20-Apul-gene-annotation.Rmd>

<https://github.com/urol-e5/deep-dive/blob/main/E-Peve/code/20-Peve-gene-annotation.Rmd>

<https://github.com/urol-e5/deep-dive/blob/main/F-Pmea/code/20-Pmea-gene-annotation.Rmd>