Sam’s Notebook: Sequencing Data – C.gigas Larvae OA

Below is a from Sam’s Lab Notebook and provides some insight into some of our genomic focused ocean acidification studies.

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 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

Metagenomics Reveals Planktonic Bacterial Community Shifts across a Natural CO2 Gradient in the Mediterranean Sea

Visit this link to see original document. See Emma’s “Acidification” bookmarks for other recent papers of interest.