Tag Archives: ocean acidification

Oyster Sampling – Olympia Oyster OA Populations at Manchester

I helped Katherine Silliman with her oyster sampling today from her ocean acidification experiment with Olympia oysters (Ostrea lurida) at the Kenneth K. Chew Center for Shellfish Research & Restoration, which is housed at the NOAA Northwest Fisheries Science Center at Manchester in a partnership with the Puget Sound Restoration Fund (PSRF). We sampled the following tissues and stored in 1mL RNAlater:

  • adductor muscle (A)
  • ctenidia (C)
  • mantle (M)

When there was sufficient ctenidia tissue, an additional sample was stored in 75% ethanol for potential microbial analysis.

Tissue was collected from two oysters from each of the following oyster populations:

  • British Columbia (BC)
  • California (CA)
  • Oregon (OR)

Oysters were sampled from each of the following tanks:

  • 1A
  • 2A
  • 3A
  • 4A
  • 1B
  • 2B
  • 3B
  • 4B

Tubes were labeled in the following fashion:

  1. Population & Tank (e.g. OR3B)
  2. Tag#
  3. Tissue

If no tag was present on the oyster, the oyster was assigned a number (beginning at 150 and increased sequentially) and photographed with a ruler for future measurement. White colored tags were written with the number followed by the letter ‘W’ (e.g. 78W) – no tag color info was recorded for other tag colors.

Additionally, gonad developmental stage was roughly assessed: ripe, kinda ripe, or not ripe.

All info was recorded by Katherine in her notepad. All samples were retained by Katherine (not sure where she stored them).

Utensils were flame sterilized between oysters and gloves/work surfaces were washed with a 10% bleach solution between oysters.

 

Here are a few pics from the day:

 

 

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Morphometrics – Olympia Oyster OA Larvae Completed

Finished measuring Ostrea lurida larvae using NIS-Elements BR (10x objective and 10x nosepiece setting in software). That’s 2,620 larvae measured!

NOTE: Robyn previously measured 33 tubes worth of larvae, but I’m not certain where that data was saved.

All measurements by me can be found here (Google Sheet): FHL_Oly_larvae_measurements

Measured 30 larvae from each tube of the following samples:

  Box Label Color Tube Label Notes
70 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 U FB HL.L-1
71 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 V FB HL.L.2
72 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 W FB HH.L.1
73 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 X FB HH.L.2
74 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 Y SS LLH3 Many transluscent shells
75 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 Z SS LL.H.4 Many transluscent shells
76 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 AA SS LHH3 Mostly transluscent shells
77 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 BB SS LHH4
78 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 CC SS LL.L.3
79 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 DD SS LL.L.4
80 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 EE SS LH.L.3
81 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 FF SS LH.L.4
82 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LLL-1 4.3.E
83 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LLL2 4.3.F
84 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LHL-1 4.3.G
85 FHL Oly OA x DO Box 2 etOH Friedman Pink 4.4.15 FB release Low CO2 103A
86 FHL Oly OA x DO Box 2 etOH Friedman White SS Low CO2 4.4.15 release 103A All shells partially transluscent.
87 FHL Oly OA x DO Box 2 etOH Friedman Blue SS High CO2 4/5-6/15 release 103B All shells mostly transluscent.
88 FHL Oly OA x DO Box 2 etOH Friedman Pink 44/5-6/15 release FB LCO2 FB 103A

 

Example images from notes above:

 

Sample #74

 

 

Sample #75

 

 

Sample #77

 

 

Sample #85

 

 

Sample #86

 

 

Sample #87

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Morphometrics – Olympia Oyster OA Larvae Continued

Continued measuring Ostrea lurida larvae using NIS-Elements BR (10x objective and 10x nosepiece setting in software).

All measurements can be found here (Google Sheet): FHL_Oly_larvae_measurements

Measured 30 larvae from each tube of the following samples:

  Box Label Color Tube Label Notes
34 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 108B LH-L-1 D5 SS
35 2015 – DO x pH Olys FHL Friedman White 3.24.15 103A-SS Olys. Low CO2 released 3.23.15 Jagged shells; See image below
36 2015 – DO x pH Olys FHL Friedman White 3.26.15 SS LL-H1 103A
37 2015 – DO x pH Olys FHL Friedman White 103A 3.26.15SS LL-H2
38 2015 – DO x pH Olys FHL Friedman White 103B 3.26.15 SS LH-H-1
39 2015 – DO x pH Olys FHL Friedman White 3.26.15 103BSS LHH-2
40 2015 – DO x pH Olys FHL Friedman White 108A 3.26.15 SS LL-L-1
41 2015 – DO x pH Olys FHL Friedman White 108A 3.26.15 SS LL-L-2
42 2015 – DO x pH Olys FHL Friedman White 108B 3.26.15 LHL-1 SS
43 2015 – DO x pH Olys FHL Friedman Purple AR 103B FB Release 3.31.15 Many transluscent shells; See image below
44 2015 – DO x pH Olys FHL Friedman Pink LCO2 FB 103A 2d 3/25/15 release 3.27.15 All transluscent shells; See image below
45 2015 – DO x pH Olys FHL Friedman Blue LCO2 SS 3.27.15 103A from 3/23/15 release All semi-transluscent shells; See image below
46 2015 – DO x pH Olys FHL Friedman Pink 3.27.15 103A FB 3.26.15 released LCO2 – 1 day old
47 2015 – DO x pH Olys FHL Friedman Purple 3.30.15 103B FB HCO2 release
48 2015 – DO x pH Olys FHL Friedman Purple 3.30.15 FB LCO2 release 103A
49 2015 – DO x pH Olys FHL Friedman Pink AS 103A-FB released 3.31.15
50 2015 – DO x pH Olys FHL Friedman Pink FB LCO2-103A released 4.1.15 4.1.15
51 2015 – DO x pH Olys FHL Friedman White SS LCO2-103A released 3.31.15 4.1.15
52 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.GG SS HLH3
53 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.HH SS HLH4
54 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LHH2 4.3.D All semi-transluscent shells; See image below
55 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LLH1 4-3-A
56 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LLH2 4-3-B
57 FHL Oly OA x DO Box 2 etOH Friedman White 4.3.15 SS LHH1 4-3-C
58 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 I HLH-1 SS
59 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 J HLH-2 SS
60 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 K HHH-1 SS
61 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 L HHH-2 SS
62 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 M HLL-1 SS
63 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 N HLL-2 SS
64 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 O HHL-1 SS
65 FHL Oly OA x DO Box 2 etOH Friedman Blue 4.3.15 P HHL-2 SS
66 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 S FB HHH-1
67 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 T FB HHH-2
68 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 Q FB HL.H-1
69 FHL Oly OA x DO Box 2 etOH Friedman Purple 4.3.15 R FB HL.H-2

 

Example images from notes above:

Sample #35

 

 

Normal shell, for comparison to jagged shell image above:

 

Sample #43 – Many transluscent shells

 

Sample #44 – All transluscent shells

 

Sample #45 – Partially transluscent shells

 

Sample #54 – All transluscent shells

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Morphometrics – Olympia Oyster OA Larvae Continued

Continued measurements of larvae samples from yesterday. Measured length (hinge to growing edge) and width of 30 oysters from each tube using NIS-Elements BR (10x objective and 10x nosepiece setting in software).

The measurement data can be found here (Google Sheet): FHL_Oly_larvae_measurements

Here’s the list of tubes that were measured today and their labels:

  Box Label Color Tube Label Notes
14 2015 – DO x pH Olys FHL Friedman White AM 103B-SS LH-H-2 3.31.15
15 2015 – DO x pH Olys FHL Friedman White AL 103B-SSLH-H-1 3.31.15
16 2015 – DO x pH Olys FHL Friedman White AK 3.31.15 103A-SS LL-H-2
17 2015 – DO x pH Olys FHL Friedman White AJ 3.31.15 108A-SS LL-H-1
18 2015 – DO x pH Olys FHL Friedman Blue AG 108A-SS HL-L-2 4.1.15
19 2015 – DO x pH Olys FHL Friedman White 3.30.15 SS-103A LL-H-3 Day 3 3.30.15
20 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS-103A LLH-4 3.30.15
21 2015 – DO x pH Olys FHL Friedman White 3.30.15 SS-103B Day 3 LH-H-3 3.30.15
22 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS 103B LHH-4 Day 3
23 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS-108A LL-L-3 3.30.15
24 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS 108A LLL-4 Day 3
25 2015 – DO x pH Olys FHL Friedman White 3.30.15 SS 108B Day 3 LHL-3 3.30.15
26 2015 – DO x pH Olys FHL Friedman White 3.30.15 Day 3 SS 108B LH-L-4 3.30.15 Day 3
27 2015 – DO x pH Olys FHL Friedman Blue AH 108B-SS HH-L-1 4.1.15
28 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5-103A LL-H1 SS-D5
29 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 103A LL-H-2 D5 SS
30 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 103B LH-H-1 SS D5
31 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5103B LH-H-2 D5 SS
32 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 108A LL-L-1 D5-SS
33 2015 – DO x pH Olys FHL Friedman White 3.29.15 Day 5 108A LL-L-2 -SS D5

 

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Morphometrics – Olympia Oyster OA Larvae

Olympia oyster larvae were measured using NIS Elements-BR (Nikon) imaging software to measure larvae length (hinge to growing edge) and width (10x objective and 10x nosepiece setting on software). Below is a screenshot of what the software, larvae, and measurement controls look like:

Measured 30 individuals from each tube.

The following samples were measured (these are the tube labels; currently not certain what shorthand labelling scheme should be used):

  Box Label Color Tube Label Notes
1 2015 – DO x pH Olys FHL Friedman White/Blue Released: 3.25.15 103B-SS Olys High CO2 3-25-15
2 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 103A HLH-1 3.28.15 3/25/release
3 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 103A HL-H-2 3.28.15 3.25 release
4 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 103B HH-H-1 3.28.15 3/25 release
5 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 103B HH-H-2 3.27.15 release
6 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 108A HL-L-1 3.27.15 3/25 release
7 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 108A HL-L2 3.27.15 3.25 release
8 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 108B HH-L-1 3.27.15 3/25 release
9 2015 – DO x pH Olys FHL Friedman Blue SS Day 3 HH-L-2 3.27.15 3.25 release
10 2015 – DO x pH Olys FHL Friedman Blue AI 108B-SS HH-L-2 4.1.15
11 2015 – DO x pH Olys FHL Friedman White Ap 108B-SS LH-L-1 3.31.15
12 2015 – DO x pH Olys FHL Friedman White AN 108A-SS LL-L-1 3.31.15
13 2015 – DO x pH Olys FHL Friedman White AO 103A-SS LL-L-2 3.31.15

Measurement data is here (Google Sheet): FHL_Oly_larvae_measurements

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Computer Setup – Dell Optiplex 960 for OA System

Dan had been using the Dell Studio XPS 7100 for running LabView to record data from the Honeywell Dual Input Controller for controlling the OA system at Manchester. The computer occasionally failed; it would shutdown, wouldn’t boot and would just produce six steady beeps. Although this behaviour was inconsistent, Dan needs a computer that will always remain on for data logging.

Our departmental computer support person couldn’t diagnose the problem and offered to provide a replacement computer, but only if we purchased a SSD drive for the replacement computer (at a cost of ~$250 for a 480GB SSD drive and adapter).

So, instead of wasting the money (and the continued headache of dealing with our computer support person), I grabbed the Dell Optiplex 980 from FSH 240, backed up the data on that computer (backed up to Nate’s folder on our server: backupordie). I obtained the appropriate license/serial numbers for LabView from the College of Engineering, downloaded and installed LabView 2014 and service pack 1 (SP1).

The old computer was able to boot, so I copied all the LabView files that Dan had previously been using to the Friedman Lab Dropbox and then downloaded them to the Dell Optiplex 980. Additionally, I re-seated the RAM sticks in hopes of making the computer usable again. I have moved this computer to FSH 240 to take the place of the Dell Optiplex 980.

Dan will take the newly configured Dell Optiplex 960 to Manchester to use as a data logger for the Honeywell Dual Input Analyzer and its pH and temp data.

 

 

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Quality Trimming – C.gigas Larvae OA BS-Seq Data

Jupyter (IPython) Notebook: 20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb

NBviewer: 20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb

 

Trimmed FASTQC

400ppm Index – GCCAAT

20150414_trimmed_2212_lane2_GCCAAT_L002_R1_001_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_002_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_003_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_004_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_005_fastqc.html
20150414_trimmed_2212_lane2_GCCAAT_L002_R1_006_fastqc.html

1000ppm Index – CTTGTA

20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc.html
20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc.html
20150414_trimmed_2212_lane2_CTTGTA_L002_R1_003_fastqc.html
20150414_trimmed_2212_lane2_CTTGTA_L002_R1_004_fastqc.html

 

 

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Sequence Data Analysis – C.gigas Larvae OA BS-Seq Data

Compared total amount of data generated from each index. The commands below send the output of the ‘ls -l’ command to awk. Awk sums the file sizes, found in the 5th field ($5) of the ‘ls -l’ command, then prints the sum, divided by 1024^3 to convert from bytes to gigabytes.

Index: CTTGTA

$ ls -l 2212_lane2_[C]* | awk '{sum += $5} END {print sum/1024/1024/1024}'
5.33341

Index: GCCAAT
$ ls -l 2212_lane2_[G]* | awk '{sum += $5} END {print sum/1024/1024/1024}'
7.00596

There’s ~1.4x data in the GCCAAT files.

 

Ran FASTQC on the following files downloaded earlier today:

2212_lane2_CTTGTA_L002_R1_001.fastq.gz
2212_lane2_CTTGTA_L002_R1_002.fastq.gz
2212_lane2_CTTGTA_L002_R1_003.fastq.gz
2212_lane2_CTTGTA_L002_R1_004.fastq.gz
2212_lane2_GCCAAT_L002_R1_001.fastq.gz
2212_lane2_GCCAAT_L002_R1_002.fastq.gz
2212_lane2_GCCAAT_L002_R1_003.fastq.gz
2212_lane2_GCCAAT_L002_R1_004.fastq.gz
2212_lane2_GCCAAT_L002_R1_005.fastq.gz
2212_lane2_GCCAAT_L002_R1_006.fastq.gz

 

The FASTQC command is below. This command runs FASTQC in a for loop over any files that begin with “2212_lane2_C” or “2212_lane2_G” and outputs the analyses to the Arabidopsis folder on Eagle:

$for file in /Volumes/nightingales/C_gigas/2212_lane2_[CG]*; do fastqc "$file" --outdir=/Volumes/Eagle/Arabidopsis/; done

 

From within the Eagle/Arabidopsis folder, I renamed the FASTQC output files to prepend today’s date:

$for file in 2212_lane2_[GC]*; do mv "$file" "20150413_$file"; done

 

Then, I unzipped the .zip files generated by FASTQC in order to have access to the images, to eliminate the need for screen shots for display in this notebook entry:

$for file in 20150413_2212_lane2_[CG]*.zip; do unzip "$file"; done

 

The unzip output retained the old naming scheme, so I renamed the unzipped folders:

$for file in 2212_lane2_[GC]*; do mv “$file” “20150413_$file”; done

 

The FASTQC results are linked below:

20150413_2212_lane2_CTTGTA_L002_R1_001_fastqc.html

20150413_2212_lane2_CTTGTA_L002_R1_002_fastqc.html
20150413_2212_lane2_CTTGTA_L002_R1_003_fastqc.html
20150413_2212_lane2_CTTGTA_L002_R1_004_fastqc.html
20150413_2212_lane2_GCCAAT_L002_R1_001_fastqc.html
20150413_2212_lane2_GCCAAT_L002_R1_002_fastqc.html
20150413_2212_lane2_GCCAAT_L002_R1_003_fastqc.html
20150413_2212_lane2_GCCAAT_L002_R1_004_fastqc.html
20150413_2212_lane2_GCCAAT_L002_R1_005_fastqc.html
20150413_2212_lane2_GCCAAT_L002_R1_006_fastqc.html

 

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Sequence Data – C.gigas OA Larvae BS-Seq Demultiplexed

I had previously contacted Doug Turnbull at the Univ. of Oregon Genomics Core Facility for help demultiplexing this data, as it was initially returned to us as a single data set with “no index” (i.e. barcode) set for any of the libraries that were sequenced. As it turns out, when multiplexed libraries are sequenced using the Illumina platform, an index read step needs to be “enabled” on the machine for sequencing. Otherwise, the machine does not perform the index read step (since it wouldn’t be necessary for a single library). Surprisingly, the sample submission form for the Univ. of Oregon Genomics Core Facility  doesn’t request any information regarding whether or not a submitted sample has been multiplexed. However, by default, they enable the index read step on all sequencing runs. I provided them with the barcodes and they demultiplexed them after the fact.

I downloaded the new, demultiplexed files to Owl/nightingales/C_gigas:

lane2_CTTGTA_L002_R1_001.fastq.gz
lane2_CTTGTA_L002_R1_002.fastq.gz
lane2_CTTGTA_L002_R1_003.fastq.gz
lane2_CTTGTA_L002_R1_004.fastq.gz
lane2_GCCAAT_L002_R1_001.fastq.gz
lane2_GCCAAT_L002_R1_002.fastq.gz
lane2_GCCAAT_L002_R1_003.fastq.gz
lane2_GCCAAT_L002_R1_004.fastq.gz
lane2_GCCAAT_L002_R1_005.fastq.gz
lane2_GCCAAT_L002_R1_006.fastq.gz

Notice that the file names now contain the corresponding index!

Renamed the files, to append the order number to the beginning of the file names:

$for file in lane2*; do mv "$file" "2212_$file"; done

New file names:

2212_lane2_CTTGTA_L002_R1_001.fastq.gz
2212_lane2_CTTGTA_L002_R1_002.fastq.gz
2212_lane2_CTTGTA_L002_R1_003.fastq.gz
2212_lane2_CTTGTA_L002_R1_004.fastq.gz
2212_lane2_GCCAAT_L002_R1_001.fastq.gz
2212_lane2_GCCAAT_L002_R1_002.fastq.gz
2212_lane2_GCCAAT_L002_R1_003.fastq.gz
2212_lane2_GCCAAT_L002_R1_004.fastq.gz
2212_lane2_GCCAAT_L002_R1_005.fastq.gz
2212_lane2_GCCAAT_L002_R1_006.fastq.gz

Updated the checksums.md5 file to include the new files (the command is written to exclude the previously downloaded files that are named “2212_lane2_NoIndex_”; the [^N] regex excludes any files that have a capital ‘N’ at that position in the file name):

$for file in 2212_lane2_[^N]*; do md5 "$file" >> checksums.md5; done

Updated the readme.md file to reflect the addition of these new files.

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Sequencing Data – C.gigas Larvae OA

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://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_001.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_002.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_003.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_004.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_005.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_006.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_007.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_008.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_009.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_010.fastq.gz
curl -O http://gcf.uoregon.edu:8080/job/download/2212?fileName=lane2_NoIndex_L002_R1_011.fastq.gz
curl -O http://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

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