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:

curl -O http://ift.tt/1C2LyLG
curl -O http://ift.tt/1Gx7FcE
curl -O http://ift.tt/1C2LATN
curl -O http://ift.tt/1Gx7FcK
curl -O http://ift.tt/1C2LATR
curl -O http://ift.tt/1Gx7D4B
curl -O http://ift.tt/1C2LBa5
curl -O http://ift.tt/1Gx7D4D
curl -O http://ift.tt/1C2LBa9
curl -O http://ift.tt/1Gx7FcS
curl -O http://ift.tt/1C2LBab
curl -O http://ift.tt/1Gx7FcU


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

from Sam’s Notebook http://ift.tt/1Gx7Fte

Sequencing Data – C.gigas Larvae OA
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