**Data**\
Existing RNA-Seq data was retrieved from the following complete RNASeq data available in the [NCBI database](https://www.ncbi.nlm.nih.gov/):\
- SRR19782039 [Exposure to Valsartan & Carbamazepine](https://www.ncbi.nlm.nih.gov/sra/SRX15826291%5Baccn%5D)\
- SRR16771870 [Exposure to a synthetic hormone 17 a-Ethinylestradiol (EE2)](https://www.ncbi.nlm.nih.gov/sra/SRX12971792%5Baccn%5D)\
- SRR7725722 [Diarrhetic Shellfish Poisoning (DSP) toxins associated with Harmful Algal Blooms (HABs)](https://www.ncbi.nlm.nih.gov/sra/SRX4582204%5Baccn%5D)\
- SRR13013756 [Hypoxia](https://www.ncbi.nlm.nih.gov/sra/SRX9464766%5Baccn%5D)\
- *Mytilus galloprovincialis* [Reference Genome](https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_900618805.1/)

### Downloading the RNASeq data from the accession numbers using SRA Toolkit
```{bash}
# Pull out all of the sequences from the exposures

/home/shared/sratoolkit.3.0.2-ubuntu64/bin/./fasterq-dump \
--outdir /home/shared/8TB_HDD_02/cnmntgna/GitHub/chris-musselcon/output/ncbi \
--progress \
SRR19782039 \
SRR13013756 \
SRR7725722 \
SRR16771870 


```

### Pulling my reference genome from prefab code provided by NCBI
```{bash}

# verify where I am working

cd ../data
ls

```
```{bash}

# grab the reference
cd ../data

curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCA_900618805.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCA_900618805.1.zip" -H "Accept: application/zip"

unzip GCA_900618805.1.zip /chris-musselcon/data 

```
### OLD Genome - not needed
```{bash}
# remove when I clean this up


cd ../data

curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCA_025277285.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCA_025277285.1.zip" -H "Accept: application/zip"

```

# Couldn't move unzip here, moved to terminal and did it
```{bash}

#couldn't make this work so I went over to terminal and did it

cd .
ls
 unzip GCA_025277285.1.zip
````

## Kallisto
### Inspect what we have first, then run Kallisto
```{bash}
# remove this code chunk but keep the one below
cd /home/shared/kallisto

```
inspect
```{bash}

head ../data/ncbi_dataset/data/GCA_900618805.1/*.fna

```

```{bash}

/home/shared/kallisto/kallisto index -h
chmod 777 ../data/ncbi_dataset/data/GCA_900618805.1/cds_from_genomic.fna

```
```{bash}

head ../data/ncbi_dataset/data/GCA_900618805.1/cds_from_genomic.fna

```
# Create the index file to align my short read files to the genes from the MGAL_10
```{bash}



/home/shared/kallisto/kallisto \
index -i \
../data/MGAL_cds.index \ 
../home/shared/8TB_HDD_01/sr320/ncbi/ncbi_dataset/data/GCA_900618805.1/cds_from_genomic.fna


```

```{r}

kallisto first
can trim with cds/ gff and use hisat if i want to 
# library(ShortRead)

# fastq <- readFastq("~/output/ncbi/SRR7725722_1.fastq")
```