---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-03-20 03:07:19+00:00
layout: post
slug: sequencing-data-c-gigas-larvae-oa
title: Sequencing Data - C.gigas Larvae OA
categories:
  - 2015
  - Crassostrea gigas larvae OA (2011) bisulfite sequencing
tags:
  - BS-seq
  - checksum
  - code
  - Crassostrea gigas
  - curl
  - HiSeq2500
  - larvae
  - md5
  - OA
  - ocean acidification
  - Pacific oyster
---

Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by [Univ. of Oregon Genomics Core Facility](https://gcf.uoregon.edu:8080/) (order number 2212).

Samples sequenced/pooled for this run:

<table >
<tbody >
<tr >

<td >**Sample**
</td>

<td >**Treatment**
</td>

<td >**Barcode**
</td>
</tr>
<tr >

<td >400ppm
</td>

<td >400ppm
</td>

<td >GCCAAT
</td>
</tr>
<tr >

<td >1000ppm
</td>

<td >1000ppm
</td>

<td >CTTGTA
</td>
</tr>
</tbody>
</table>



All code listed below was run on OS X 10.9.5

Ran a bash script called "download.sh" to download all the files. The script contents were:

`#!/bin/bash
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_001.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_002.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_003.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_004.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_005.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_006.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_007.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_008.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_009.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_010.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_011.fastq.gz
curl -O https://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_012.fastq.gz`



Downloaded all 12 fastq.gz files to [Owl/web/nightingales/C_gigas](https://owl.fish.washington.edu/nightingales/C_gigas/)

Renamed all files by removing the beginning of each file name (2112?fileName=) and replacing that with 2212_:

`$for file in 2212*lane2_NoIndex_L002_R1_0*; do mv "$file" "${file/#2212?fileName=/2212_}"; done`



Created a directory readme.md (markdown) file to list & describe directory contents: [readme.md](https://owl.fish.washington.edu/nightingales/C_gigas/readme.md)

`$ls *.gz >> readme.md`

Note: In order for the readme file to appear in the web directory listing, the file cannot be all upper-case.



Create MD5 checksums for each the files: [checkums.md5](https://owl.fish.washington.edu/nightingales/C_gigas/checksums.md5)

`$md5 2212* >> checksums.md5`
