Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility (order number 2112).
Samples sequenced/pooled for this run:
| Sample | Treatment | Barcode |
| HB2 | 25,000ppm oil | ATCACG |
| HB16 | 25,000ppm oil | TTAGGC |
| HB30 | 25,000ppm oil | TGACCA |
| NB3 | No oil | ACAGTG |
| NB6 | No oil | GCCAAT |
| NB11 | No oil | CAGATC |
All code listed below was run on OS X 10.9.5
Downloaded all 15 fastq.gz files to Owl/web/nightingales/C_virginica:
$curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_001.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_002.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_003.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_004.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_005.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_006.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_007.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_008.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_009.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_010.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_011.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_012.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_013.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_014.fastq.gz $curl -O https://gcf.uoregon.edu:8080/job/download/2112?fileName=lane1_NoIndex_L001_R1_015.fastq.gz
Renamed all files by removing the beginning of each file name (2112?fileName=) and replacing that with 2112_:
$for file in 2112*lane1_NoIndex_L001_R1_0*; do mv "$file" "${file/#2112?fileName=/2112_}"; 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.
Created MD5 checksums for each fastq.gz file: checksums.md5
$md5 *.gz >> checksums.md5