---
title: "00.21-D-Apul-BS-genome"
author: "Sam White"
date: "2025-01-02"
output: 
  bookdown::html_document2:
    theme: cosmo
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
  github_document:
    toc: true
    number_sections: true
  html_document:
    theme: cosmo
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
bibliography: references.bib
---

# Background

This Rmd file will create a bisulfite-converted genome by, and for, Bismark [@krueger2011] using the `Apulchra-genome.fa` file. The genome FastA was taken from the [deep-dive-expression Wiki](https://github.com/urol-e5/deep-dive-expression/wiki/00-Genomic-Resources#acropora-pulchra) (GitHub Wiki), but I'm not sure of its exact origin.

Due to large sizes of output files, the files cannot be sync'd to GitHub. As such, the output directories will be gzipped and available here:

- [https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/Apulchra-genome-bisulfite.tar.gz](https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/Apulchra-genome-bisulfite.tar.gz) (1.3GB)

- [https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/Apulchra-genome-bisulfite.tar.gz.md5](https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/Apulchra-genome-bisulfite.tar.gz.md5)

  - MD5: `9e1db5875f210007a43e2083f01c2db9`

# Inputs

- Directory containing a FastA file with the file extension: .fa or .fasta (also ending in .gz).

# Outputs

- CT Conversion

  - Bowtie2 index files.
  - CT conversion FastA
  
- GA conversion

  - Bowtie2 index files.
  - GA conversion FastA.

```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,        # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  comment = ""         # Prevents appending '##' to beginning of lines in code output
)
```

# Create a Bash variables file

This allows usage of Bash variables across R Markdown chunks.

```{r save-bash-variables-to-rvars-file, engine='bash', eval=TRUE}
{
echo "#### Assign Variables ####"
echo ""

echo "# Data directories"
echo 'export timeseries_dir=/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular'
echo 'export output_dir_top=${timeseries_dir}/D-Apul/data'
echo 'export genome_dir=${timeseries_dir}/D-Apul/data'
echo ""

echo "# Paths to programs"
echo 'export programs_dir="/home/shared"'
echo 'export bismark_dir="${programs_dir}/Bismark-0.24.0"'
echo 'export bowtie2_dir="${programs_dir}/bowtie2-2.4.4-linux-x86_64"'
echo ""

echo "# Set number of CPUs to use"
echo 'export threads=20'
echo ""

echo "# Print formatting"
echo 'export line="--------------------------------------------------------"'
echo ""
} > .bashvars

cat .bashvars
```

# Bisfulite conversion

```{r bismark-genome-conversion, engine='bash', eval=FALSE}
# Load bash variables into memory
source .bashvars

${bismark_dir}/bismark_genome_preparation \
${genome_dir} \
--parallel ${threads} \
--bowtie2 \
--path_to_aligner ${bowtie2_dir}
```

# Inpect BS output
```{r inspect-BS-output, engine='bash', eval=TRUE}
# Load bash variables into memory
source .bashvars

tree -h ${genome_dir}/Bisulfite_Genome
```

# REFERENCES