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

Since we've got trimmed input fastq files and a prepped genome, it's time to start the alignment. This is the slow step, but the files aren't super huge/there arenlt a ton, so hopefully this will only take a few days.

```{r}

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

bismark.genome <- "~/Documents/C-virginica-BSSeq/genome"

trimmed.input.files <- list.files(pattern = "*.trimmed.fq")

for(i in 1:length(trimmed.input.files))   {
  
   system(paste0("/home/shared/Bismark/bismark --multicore 9 -N 1 -q --genome ", bismark.genome, " --se ", trimmed.input.files[i], " -o ~/Documents/C-virginica-BSSeq/", substr(trimmed.input.files[i], 1, 17)))
  
}


```