---
title: "01-genome"
format: html
editor: visual
---

# Look at genome

Lets look at genome and prepare for bismark (program for methylation)

```{bash}
cd ../data

curl -O https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/965/363/235/GCA_965363235.1_xbMytGall1.hap1.1/GCA_965363235.1_xbMytGall1.hap1.1_genomic.fna.gz


```

```{bash}
gunzip ../data/GCA_965363235.1_xbMytGall1.hap1.1_genomic.fna.gz

```

```{bash}
head ../data/GCA_965363235.1_xbMytGall1.hap1.1_genomic.fna 
```

```{bash}
grep -c ">" ../data/GCA_965363235.1_xbMytGall1.hap1.1_genomic.fna 
```

# bismark

```{bash}
# Directories and programs
bismark_dir="/home/shared/Bismark-0.24.0"
bowtie2_dir="/home/shared/bowtie2-2.4.4-linux-x86_64/"
genome_folder="../data/"

${bismark_dir}/bismark_genome_preparation \
--verbose \
--parallel 4 \
--path_to_aligner ${bowtie2_dir} \
${genome_folder}
```

#Sequence reads

```{bash}

cd ../data

curl -O "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/project-chilean-mussel/data/Raw_WGBS_Mch/LCo_BSr1%20(paired,%20sampled)_R1.fastq"


```

```{bash}

cd ../data

curl -O "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/project-chilean-mussel/data/Raw_WGBS_Mch/LCo_BSr1%20(paired,%20sampled)_R2.fastq"


```

Preparing Chilean Genome

```{bash}
# Directories and programs
bismark_dir="/home/shared/Bismark-0.24.0"
bowtie2_dir="/home/shared/bowtie2-2.4.4-linux-x86_64/"
genome_folder="../data/Mchi/"

${bismark_dir}/bismark_genome_preparation \
--verbose \
--parallel 4 \
--path_to_aligner ${bowtie2_dir} \
${genome_folder}
```

```{bash}

cd ../data

curl -O "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/project-chilean-mussel/data/Raw_WGBS_Mch/LCo_BSr1%20(paired,%20sampled)_R1.fastq"


```

```{bash}

cd ../data

curl -O "https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/project-chilean-mussel/data/Raw_WGBS_Mch/LCo_BSr1%20(paired,%20sampled)_R2.fastq"


```

\`\`\`

Aligning reads
