Sequencing Data - C.gigas Larvae OA

2015
Crassostrea gigas larvae OA (2011) bisulfite sequencing
BS-seq
checksum
code
Crassostrea gigas
curl
HiSeq2500
larvae
md5
OA
ocean acidification
Pacific oyster
Author

Sam White

Published

March 19, 2015

Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility(order number 2212).

Samples sequenced/pooled for this run:

Sample Treatment Barcode
400ppm 400ppm GCCAAT
1000ppm 1000ppm CTTGTA

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

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

$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

$md5 2212* >> checksums.md5