---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-04-14 05:53:30+00:00
layout: post
slug: sequence-data-analysis-lsu-c-virginica-oil-spill-mbd-bs-seq-data
title: Sequence Data Analysis - LSU C.virginica Oil Spill MBD BS-Seq Data
categories:
  - 2015
  - LSU C.virginica Oil Spill MBD BS Sequencing
tags:
  - BS-seq
  - Crassostrea virginica
  - Eastern oyster
  - FASTQC
  - LSU
  - MBD-Seq
  - NGS sequencing
  - oil
---

Performed some rudimentary data analysis on the new, demultiplexed data downloaded earlier today:

2112_lane1_ACAGTG_L001_R1_001.fastq.gz
2112_lane1_ACAGTG_L001_R1_002.fastq.gz
2112_lane1_ATCACG_L001_R1_001.fastq.gz
2112_lane1_ATCACG_L001_R1_002.fastq.gz
2112_lane1_ATCACG_L001_R1_003.fastq.gz
2112_lane1_CAGATC_L001_R1_001.fastq.gz
2112_lane1_CAGATC_L001_R1_002.fastq.gz
2112_lane1_CAGATC_L001_R1_003.fastq.gz
2112_lane1_GCCAAT_L001_R1_001.fastq.gz
2112_lane1_GCCAAT_L001_R1_002.fastq.gz
2112_lane1_TGACCA_L001_R1_001.fastq.gz
2112_lane1_TTAGGC_L001_R1_001.fastq.gz
2112_lane1_TTAGGC_L001_R1_002.fastq.gz



Compared total amount of data (in gigabytes) 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: ACAGTG

`$ls -l 2112_lane1_AC* | awk '{sum += $5} END {print sum/1024/1024/1024}'
1.49652`



Index: ATCACG

`$ls -l 2112_lane1_AT* | awk '{sum += $5} END {print sum/1024/1024/1024}'
3.02269`



Index: CAGATC

`$ls -l 2112_lane1_CA* | awk '{sum += $5} END {print sum/1024/1024/1024}'
3.49797`



Index: GCCAAT

`$ls -l 2112_lane1_GC* | awk '{sum += $5} END {print sum/1024/1024/1024}'
2.21379`



Index: TGACCA

`$ls -l 2112_lane1_TG* | awk '{sum += $5} END {print sum/1024/1024/1024}'
0.687374`



Index: TTAGGC

`$ls -l 2112_lane1_TT* | awk '{sum += $5} END {print sum/1024/1024/1024}'
2.28902`



Ran FASTQC on the following files downloaded earlier today. 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:

`$for file in /Volumes/nightingales/C_virginica/2112_lane1_[ATCG]*; do fastqc "$file" --outdir=/Volumes/Eagle/Arabidopsis/; done`



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

`$for file in 2112_lane1_[ATCG]*; do mv "$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:

`$for file in 20150413_2112_lane1_[ATCG]*.zip; do unzip "$file"; done`



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

`$for file in 2112_lane1_[ATCG]*; do mv "$file" "20150413_$file"; done`



The FASTQC results are linked below:

[20150413_2112_lane1_ACAGTG_L001_R1_001_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_ACAGTG_L001_R1_001_fastqc.html)
[20150413_2112_lane1_ACAGTG_L001_R1_002_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_ACAGTG_L001_R1_002_fastqc.html)
[20150413_2112_lane1_ATCACG_L001_R1_001_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_ATCACG_L001_R1_001_fastqc.html)
[20150413_2112_lane1_ATCACG_L001_R1_002_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_ATCACG_L001_R1_002_fastqc.html)
[20150413_2112_lane1_ATCACG_L001_R1_003_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_ATCACG_L001_R1_003_fastqc.html)
[20150413_2112_lane1_CAGATC_L001_R1_001_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_CAGATC_L001_R1_001_fastqc.html)
[20150413_2112_lane1_CAGATC_L001_R1_002_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_CAGATC_L001_R1_002_fastqc.html)
[20150413_2112_lane1_CAGATC_L001_R1_003_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_CAGATC_L001_R1_003_fastqc.html)
[20150413_2112_lane1_GCCAAT_L001_R1_001_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_GCCAAT_L001_R1_001_fastqc.html)
[20150413_2112_lane1_GCCAAT_L001_R1_002_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_GCCAAT_L001_R1_002_fastqc.html)
[20150413_2112_lane1_TGACCA_L001_R1_001_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_TGACCA_L001_R1_001_fastqc.html)
[20150413_2112_lane1_TTAGGC_L001_R1_001_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_TTAGGC_L001_R1_001_fastqc.html)
[20150413_2112_lane1_TTAGGC_L001_R1_002_fastqc.html](https://eagle.fish.washington.edu/Arabidopsis/20150413_2112_lane1_TTAGGC_L001_R1_002_fastqc.html)


