---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-04-14 05:53:13+00:00
layout: post
slug: sequence-data-analysis-c-gigas-larvae-oa-bs-seq-data
title: Sequence Data Analysis - C.gigas Larvae OA BS-Seq Data
categories:
  - 2015
  - Crassostrea gigas larvae OA (2011) bisulfite sequencing
tags:
  - BS-seq
  - Crassostrea gigas
  - FASTQC
  - larvae
  - NGS sequencing
  - OA
  - ocean acidification
  - Pacific oyster
---

Compared total amount of data generated from each index. The commands below send the output of the 'ls -l' command to awk. Awk sums the file sizes, found in the 5th field ($5) of the 'ls -l' command, then prints the sum, divided by 1024^3 to convert from bytes to gigabytes.

Index: CTTGTA

`$ ls -l 2212_lane2_[C]* | awk '{sum += $5} END {print sum/1024/1024/1024}'
5.33341`

Index: GCCAAT
`$ ls -l 2212_lane2_[G]* | awk '{sum += $5} END {print sum/1024/1024/1024}'
7.00596`

There's ~1.4x data in the GCCAAT files.



Ran FASTQC on the following files downloaded earlier today:

2212_lane2_CTTGTA_L002_R1_001.fastq.gz
2212_lane2_CTTGTA_L002_R1_002.fastq.gz
2212_lane2_CTTGTA_L002_R1_003.fastq.gz
2212_lane2_CTTGTA_L002_R1_004.fastq.gz
2212_lane2_GCCAAT_L002_R1_001.fastq.gz
2212_lane2_GCCAAT_L002_R1_002.fastq.gz
2212_lane2_GCCAAT_L002_R1_003.fastq.gz
2212_lane2_GCCAAT_L002_R1_004.fastq.gz
2212_lane2_GCCAAT_L002_R1_005.fastq.gz
2212_lane2_GCCAAT_L002_R1_006.fastq.gz



The FASTQC command is below. This command runs FASTQC in a for loop over any files that begin with "2212_lane2_C" or "2212_lane2_G" and outputs the analyses to the Arabidopsis folder on Eagle:

`$for file in /Volumes/nightingales/C_gigas/2212_lane2_[CG]*; do fastqc "$file" --outdir=/Volumes/Eagle/Arabidopsis/; done`



From within the Eagle/Arabidopsis folder, I renamed the FASTQC output files to prepend today's date:

`$for file in 2212_lane2_[GC]*; do mv "$file" "20150413_$file"; done`



Then, I unzipped the .zip files generated by FASTQC in order to have access to the images, to eliminate the need for screen shots for display in this notebook entry:

`$for file in 20150413_2212_lane2_[CG]*.zip; do unzip "$file"; done`



The unzip output retained the old naming scheme, so I renamed the unzipped folders:

$for file in 2212_lane2_[GC]*; do mv "$file" "20150413_$file"; done



The FASTQC results are linked below:
[
20150413_2212_lane2_CTTGTA_L002_R1_001_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_CTTGTA_L002_R1_001_fastqc.html)
[20150413_2212_lane2_CTTGTA_L002_R1_002_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_CTTGTA_L002_R1_002_fastqc.html)
[20150413_2212_lane2_CTTGTA_L002_R1_003_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_CTTGTA_L002_R1_003_fastqc.html)
[20150413_2212_lane2_CTTGTA_L002_R1_004_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_CTTGTA_L002_R1_004_fastqc.html)
[20150413_2212_lane2_GCCAAT_L002_R1_001_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_GCCAAT_L002_R1_001_fastqc.html)
[20150413_2212_lane2_GCCAAT_L002_R1_002_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_GCCAAT_L002_R1_002_fastqc.html)
[20150413_2212_lane2_GCCAAT_L002_R1_003_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_GCCAAT_L002_R1_003_fastqc.html)
[20150413_2212_lane2_GCCAAT_L002_R1_004_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_GCCAAT_L002_R1_004_fastqc.html)
[20150413_2212_lane2_GCCAAT_L002_R1_005_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_GCCAAT_L002_R1_005_fastqc.html)
[20150413_2212_lane2_GCCAAT_L002_R1_006_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2212_lane2_GCCAAT_L002_R1_006_fastqc.html)