---
title: "05-bismark-cov"
output: html_document
date: "2024-11-11"
---

Taking the `-u 10000` bismark run (04)

and getting coverage file with


```{bash}
gunzip ../output/04-bismark-pipeline/*deduplicated.bismark.cov.gz
```

```{bash}
gzip ../output/04-bismark-pipeline/*deduplicated.bismark.cov
```


```{bash}
find ../output/04-bismark-pipeline/*deduplicated.bismark.cov.gz \
| xargs basename -s _1_bismark_bt2_pe.deduplicated.bismark.cov.gz \
| xargs -I{} coverage2cytosine \
--genome_folder ../output/01-bismark-init/ \
-o ../output/05-bismark-cov/{} \
--merge_CpG \
--zero_based \
../output/04-bismark-pipeline/{}_1_bismark_bt2_pe.deduplicated.bismark.cov.gz \
> ../output/05-bismark-cov/stdout.log 2> ../output/05-bismark-cov/stderr.log
```

```{bash}
find ../output/04-bismark-pipeline/*deduplicated.bismark.cov.gz \
-exec sh -c 'gunzip "{}" && gzip "${0%.gz}"' {} \;
```


```{bash}
find ../output/04-bismark-pipeline/*deduplicated.bismark.cov.gz \
| sed 's|.*/||; s/_bismark_bt2_pe.deduplicated.bismark.cov.gz$//' \
| xargs -I{} sh -c 'coverage2cytosine \
    --genome_folder ../output/01-bismark-init/ \
    -o ../output/05-bismark-cov/{}.CpG_report.txt \
    --merge_CpG \
    --zero_based \
    ../output/04-bismark-pipeline/{}_bismark_bt2_pe.deduplicated.bismark.cov.gz' \
    > ../output/05-bismark-cov/stdout.log 2> ../output/05-bismark-cov/stderr.log
```

---


try something else

```{bash}
#dedup

find ../output/01-bismark-init/*.bam | \
xargs basename -s .bam | \
xargs -I{} deduplicate_bismark \
--bam \
--paired \
../ouput/01-bismark-init/{}.bam \
> ../output/05-bismark-cov/test
```

# extract 

bismark_methylation_extractor \
--bedGraph \
--counts \
--comprehensive \
--merge_non_CpG \
--multicore 28 \
--buffer_size 75% \
*deduplicated.bam
```