---
title: "01.2-data-explore"
output: md_document
---

```{r}
library(tidyverse)
```




![img](img/ncbi.png)

```{r schemat, echo = FALSE, out.width = "70%", fig.align = "center"}
knitr::include_graphics("img/ncbi.png")
```


https://www.ncbi.nlm.nih.gov/sra?term=c


```{bash}
/home/shared/sratoolkit.2.11.2-ubuntu64/bin/fasterq-dump.2.11.2 \
--outdir ../data  \
--split-files \
--threads 27 \
--mem 100GB \
--progress \
SRR8788211
```

/home/shared/sratoolkit.2.11.2-ubuntu64/bin/fasterq-dump.2.11.2 \
--outdir . \
--split-files \
--threads 27 \
--mem 100GB \
--progress \
SRR12212519


```{bash}
/home/shared/sratoolkit.2.11.2-ubuntu64/bin/fasterq-dump.2.11.2 \
--outdir ../data  \
--split-files \
--threads 27 \
--mem 100GB \
--progress \
SRR12227929
```


#fastqc 

```{bash}
/home/shared/FastQC/fastqc \
../data/SRR8788211_1.fastq \
../data/SRR8788211_2.fastq \
../data/SRR12227929_1.fastq \
../data/SRR12227929_2.fastq \
-t 48 \
-o ../output/01.2-data-explore/
```


```
/home/shared/MultiQC.v1.12.dev0/multiqc ../output/01.2-data-explore/
```

# Genome 

https://gannet.fish.washington.edu/Atumefaciens/20191105_swoose_pgen_v074_renaming/Panopea-generosa-v1.0.fa


```{bash}
cd ../data/ 
curl -O https://gannet.fish.washington.edu/Atumefaciens/20191105_swoose_pgen_v074_renaming/Panopea-generosa-v1.0.fa
```



```{bash}
cd ../data/ 
curl -O https://gannet.fish.washington.edu/Atumefaciens/20191105_swoose_pgen_v074_renaming/Panopea-generosa-v1.0.fa
```


```{bash}
cd ../data/ 
curl -O https://gannet.fish.washington.edu/Atumefaciens/20191105_swoose_pgen_v074_renaming/Panopea-generosa-v1.0.a4.gene.gff3
```


# Transcriptome

http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_transcriptome_v5.fasta

https://gannet.fish.washington.edu/Atumefaciens/20191105_swoose_pgen_v074_renaming/Panopea-generosa-v1.0.a4.gene.gff3


```{bash}
cd ../data/ 
curl -O http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_transcriptome_v5.fasta
```

```{bash}
head ../data/Pgenerosa_transcriptome_v5.fasta
```

```{bash}
grep '>' ../data/Pgenerosa_transcriptome_v5.fasta | wc -l
```


# Get gene from genome 

```{bash}
/home/shared/bedtools2/bin/fastaFromBed \
-fi ../data/Panopea-generosa-v1.0.fa \
-bed ../data/Panopea-generosa-v1.0.a4.gene.gff3 \
> ../output/01.2-data-explore/test.fa

```


