---
title: "Grabbing Needed data"
output: md_document
---


```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
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
)
```



There are several key data tables to look at deep expression of tissue.
I will provide urls here as in most cased will / could read into R from url.

# Expression data 
- https://raw.githubusercontent.com/sr320/paper-geoduck-gene-exp/main/data/salmon.merged.gene_tpm.tsv

# Gene Annotation
- https://raw.githubusercontent.com/RobertsLab/code/master/r_projects/sam/20230328-pgen-gene_annotation-update/outputs/02-goslim-mapping/20230329-pgen-annotations-SwissProt-GO-BP_GOslim.tab

more info at https://github.com/RobertsLab/resources/issues/1602

# Other clam genomes


```{r schemat}
knitr::include_graphics("img/ncbi-clam.png")
```

URL https://www.ncbi.nlm.nih.gov/data-hub/genome/?taxon=6580

## Ruditapes philippinarum
https://www.ncbi.nlm.nih.gov/data-hub/taxonomy/129788/

mRNA

```{bash}
head ../data/Rphil-mrna.fa
```

how to get that https://d.pr/i/eARMYF

## Archivesica marissinica
```{bash}
cd ../data
curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCA_014843695.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCA_014843695.1.zip" -H "Accept: application/zip"
```

```{bash}
cd ../data
unzip GCA_014843695.1.zip
```

Genome only

## Mactra quadrangularis
```{bash}
cd ../data
/home/shared/datasets \
download genome accession GCA_025267735.1 \
--include gff3,rna,cds,protein,genome,seq-report --filename GCA_025267735.1.zip
```


```{bash}
cd ../data
unzip GCA_025267735.1.zip
```


## Spisula solida
```{bash}
cd ../data
/home/shared/datasets \
download genome accession GCA_947247005.1 \ --include gff3,rna,cds,protein,genome,seq-report \ --filename GCA_947247005.1.zip
```


## Mercenaria mercenaria
paper https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-08262-1#availability-of-data-and-materials


```{bash}
cd ../data
/home/shared/datasets \
download genome accession GCF_021730395.1 --include gff3,rna,cds,protein,genome,seq-report --filename GCF_021730395.1.zip
```
