peak.cov.pipeline.Rmd

---
title: "Pipeline for peak coverage"
author: "Briana Mittleman"
date: "7/26/2018"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

I need to create a processing pipeline that I can run each time I get more individuals that will do the following:  

* combine all total and nuclear libraries (as a bigwig/genome coverage)

* call peaks with Yang's script  

* filter peaks with Yang's script  

* clean peaks

* run feature counts on these peaks for all fo the individuals  



##Create bedgraph and bigwig:  

I can do this step in my snakefile. First, I added the following to my environemnt.  

* ucsc-bedgraphtobigwig  
* ucsc-bigwigmerge  
* ucsc-wigtobigwig  
* ucsc-bigwigtobedgraph  

I want to create bedgraph for each file. I will add a rule to my snakefile that does this and puts them in the bedgraph directory.  

```{bash, eval=F}
#add to directory
dir_bedgraph= dir_data + "bedgraph/"

#add to rule_all  

expand(dir_bedgraph + "{samples}.bg", samples=samples)

#rule
rule bedgraph: 
  input:
    bam = dir_sort + "{samples}-sort.bam"
  output: dir_bedgraph + "{samples}.bg"
  shell: "bedtools genomecov -ibam {input.bam} -bg -5 > {output}"
```

I want to add more memory for this rule in the cluster.json  

```{bash, eval=F}
"bedgraph" :
    {
            "mem": 16000
    }
```


I will use the bedgraphtobigwig tool.

```{bash, eval=F}
#add to directory
dir_bigwig= dir_data + "bigwig/"
dir_sortbg= dir_data + "bedgraph_sort/"

#add to rule_all  
expand(dir_sortbg + "{samples}.sort.bg", samples=samples)
expand(dir_bigwig + "{samples}.bw", samples=samples)

rule sort_bg:
    input: dir_bedgraph + "{samples}.bg"
    output: dir_sortbg + "{samples}.sort.bg"
    shell: "sort -k1,1 -k2,2n {input} > {output}"

rule bg_to_bw:
    input: 
        bg=dir_sortbg + "{samples}.sort.bg"
        len= chrom_length 
    output: dir_bigwig + "{samples}.bw"
    shell: "bedGraphToBigWig {input.bg} {input.len} {output}""
```

##Merge BW

This next step will take all of the files in the bigwig directory and merge them. To do this I will create a script that creates a list of all of the files then uses this list in the merge script.

mergeBW.sh  

```{bash, eval=F}
#!/bin/bash

#SBATCH --job-name=mergeBW
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=mergeBW.out
#SBATCH --error=mergeBW.err
#SBATCH --partition=broadwl
#SBATCH --mem=40G
#SBATCH --mail-type=END

module load Anaconda3
source activate three-prime-env

ls -d -1 $PWD/* /project2/gilad/briana/threeprimeseq/data/bigwig | tail -n +2 > /project2/gilad/briana/threeprimeseq/data/list_bw/list_of_bigwig.txt

bigWigMerge -inList /project2/gilad/briana/threeprimeseq/data/list_bw/list_of_bigwig.txt /project2/gilad/briana/threeprimeseq/data/mergedBW/merged_combined_YL-SP-threeprimeseq.bg

```

The result of this script will be a merged bedgraph of all of the files.