---
title: "08-Apul bismark"
author: Steven Roberts
date: "`r format(Sys.time(), '%d %B, %Y')`"  
output: 
  html_document:
    theme: readable
    highlight: zenburn
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
---

```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center" # Align plots to the center
)
```


Sam did alingment


```{bash}
ls /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark 
```




#dedup

```{bash}
find /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark/*.bam | \
xargs -n 1 basename -s _R1_001.fastp-trim_bismark_bt2_pe.bam | \
parallel -j 8 deduplicate_bismark \
--bam \
--paired \
--output_dir ../output/15-Apul-bismark \
/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark//{}_R1_001.fastp-trim_bismark_bt2_pe.bam
```








```{bash}
find ../output/15-Apul-bismark/*deduplicated.bam | \
xargs basename -s _R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam | \
xargs -I{} samtools \
sort --threads 24 \
../output/15-Apul-bismark/{}_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam \
-o ../output/15-Apul-bismark/{}.sorted.bam
```

# methylation exraction

```
find ../output/09-meth-quant/*deduplicated.bam | xargs -n 1 -I{} /home/shared/Bismark-0.24.0/bismark_methylation_extractor --bedGraph --counts --comprehensive --merge_non_CpG --multicore 24 --buffer_size 75% --output ../output/09-meth-quant {} 
```

```{bash}
find ../output/15-Apul-bismark/*deduplicated.bam | xargs -n 1 -I{} \
bismark_methylation_extractor --bedGraph --counts --comprehensive --merge_non_CpG \
--multicore 24 --buffer_size 75% --output ../output/15-Apul-bismark "{}"
```

# Methylation call

```
find ../output/09-meth-quant/*deduplicated.bismark.cov.gz | \
xargs -n 1 basename -s _pe.deduplicated.bismark.cov.gz | \
parallel -j 48 /home/shared/Bismark-0.24.0/coverage2cytosine \
--genome_folder ../data/ \
-o ../output/09-meth-quant/{} \
--merge_CpG \
--zero_based \
../output/09-meth-quant/{}_pe.deduplicated.bismark.cov.gz
```

```{bash}
find ../output/15-Apul-bismark/*deduplicated.bismark.cov.gz | \
xargs -n 1 basename -s _pe.deduplicated.bismark.cov.gz | \
parallel -j 24 coverage2cytosine \
--genome_folder /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ \
-o ../output/15-Apul-bismark/{} \
--merge_CpG \
--zero_based \
../output/15-Apul-bismark/{}_pe.deduplicated.bismark.cov.gz
```

```{bash}
head ../output/15-Apul-bismark/1H3*evidence.cov
```