---
title: "Bisulfite treated C. virginica analysis pt.2"
output: html_notebook
---

My previous notebook entry contains the file manipulation parts, as well as creating and prepping the genome index for Bismark. This section will mostly contain quality trimming and analysis steps.

First, lets run some fastQC. 

```{r}

setwd("~/Documents/C-virginica-BSSeq/")

system("mkdir untrimmed_fastqc")

raw.file.list <- list.files(pattern = "*.fastq")

for(i in 1:length(raw.file.list))   {
  
  system(paste0("fastqc ", raw.file.list[i], " -o ~/Documents/C-virginica-BSSeq/untrimmed_fastqc"))
  
  
}
```


Then do some trimming with Trimmomatic. Trimmomatic is nice in that it runs FastQC on the trimmed portions in line. Saves a step!
```{r}

setwd("~/Documents/C-virginica-BSSeq/")

system("mkdir ~/Documents/C-virginica-BSSeq/trimmed_fastqc")

raw.file.list <- raw.file.list[1:6]

for(i in 1:length(raw.file.list))   {
system(paste0("/home/shared/trimgalore/trim_galore --fastqc --fastqc_args \" -o ~/Documents/C-virginica-BSSeq/trimmed_fastqc/ \" -q 20 ~/Documents/C-virginica-BSSeq/", raw.file.list[i]))

}  
```