---
title: "03-Mchi-align"
output: html_document
date: "2025-07-24"
---

align

```{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/"
reads_dir="../data/"

 ${bismark_dir}/bismark \
--path_to_bowtie ${bowtie2_dir} \
-genome ${genome_folder} \
-p 4 \
-score_min L,0,-0.6 \
-1 ${reads_dir}LCo_BSr1_R1.fastq \
-2 ${reads_dir}LCo_BSr1_R2.fastq \
-o ../output/03-Mchi-align/
```









DEduplicate


```{bash}
# Directories and programs
bismark_dir="/home/shared/Bismark-0.24.0"

cd ../output/03-Mchi-align

find *.bam | \
xargs basename -s .bam | \
xargs -I{} ${bismark_dir}/deduplicate_bismark \
--bam \
--paired \
{}.bam
```



