Sam’s Notebook:FastQC/MultiQC – C. virginica MBD BS-seq Data


Per Steven’s GitHub Issues request, I ran FastQC on the Eastern oyster MBD bisulfite sequencing data we recently got back from ZymoResearch.

Ran FastQC locally with the following script:

  #!/bin/bash /home/sam/software/FastQC/fastqc \ --threads 18 \ --outdir /home/sam/20180409_fastqc_Cvirginica_MBD \ /mnt/owl/nightingales/C_virginica/zr2096_10_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_10_s1_R2.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_1_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_1_s1_R2.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_2_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_2_s1_R2.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_3_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_3_s1_R2.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_4_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_4_s1_R2.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_5_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_5_s1_R2.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_6_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_6_s1_R2.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_7_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_7_s1_R2.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_8_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_8_s1_R2.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_9_s1_R1.fastq.gz \ /mnt/owl/nightingales/C_virginica/zr2096_9_s1_R2.fastq.gz  

MultiQC was then run on the FastQC output files.

All files were moved to Owl after the jobs completed.


FastQC Output folder: 20180409_fastqc_Cvirginica_MBD/

MultiQC Output folder: 20180409_fastqc_Cvirginica_MBD/multiqc_data/

MultiQC report (HTML): 20180409_fastqc_Cvirginica_MBD/multiqc_data/multiqc_report.html

Everything looks good to me.

Steven’s interested in seeing what the trimmed output would look like (and, how it would impact mapping efficiencies). Will initiate trimming.

See the GitHub issue linked above for the full discussion.

from Sam’s Notebook

Laura’s Notebook: Whoa, April Goals

Things have gotten away from me the past few weeks due to my Manchester experiment & planning for AU. Here is my to-do list, hoping this will help me re-group:

Manchester project

  • Finish building silos (ASAP)
  • Consider imaging larvae for size comparisons (from count subsamples), or preserve some in ethanol for future …
  • Continue daily maintenance: daily counts, wter changes, finish stocking all silos, preserved for lipid analysis
  • Compile expenses
  • Follow up with dude from NSA conference re: lipid/glycogen assay
  • Develop undergrad assistant schedule w/ Duncan, Heather

Geoduck paper

  • Email Micah re: exact dates probes were in water & geoduck were in water, chlorophyll data from summer 2017, more precise initial size values
  • Address Emma’s input
  • Re-write discussion
  • Re-analyze environmental data:
    • As per Micah’s responses to above questions (f needed)
    • stat on daily mean and daily variance dataframes
  • Send revision to Micah, Alex, Dave-o


  • Finalize experiment plan
    • I’ve proposed several experiment ideas to Abigail & Wayne, and due to time/facility constraints and lots of overlap with Wayne’s research/work already in progress, this is what we’re landing on:
      • Study the flat oyster, Ostrea angasi.
      • Questions:
        • How does O. angasi shift from nutrient storage (glycogen storage) to utilization for reproduction?
        • Does insulin-like peptide expression correlate with gonad stage? (pending Abigail’s input)
        • For like-sex/stage animals, does provisioning differ by latitude? Does glycogen content vary by temperature?
      • Sample oysters from several farms along New South Wales estuaries in which flats are currently cultivated. Oysters will all be from the same hatchery-produced “batch” (according to Wayne). Measure glycogen/lipid content in gonad, and/or glycogen-synthase / glycogen-phosphorylase. Measure insulin-like peptide expression, if possible, as these are thought to regulate metabolism, growth, reproduction. Abigail is investigating this in other, non-molluscan species.
    • Temperature and salinity sensors have been deployed at the NSW farms, and Wayne said that I will have access to at least 6 months of data for the northern- and southern-most estuaries (Camden Haven and Pambula).
    • See if I can get chlorophyll data from satelite images along NSW coastline
    • Figure out if I can do a short larval rearing experiment with brood collected from each farm – hypothesis is that warmer sites = less glycogen storage capabilities in gonad = less provisioned eggs = less larval viability.
  • Submit visa app
  • Purchase plane ticket
  • Figure out car situation – purchase used? Lease?

Polydora paper

  • Incorporate feedback from Julieta, Heather
  • Add final touches / missing info
  • Invite input/co-authors: Steven, Brent, PCSGA rep, WDFW, hatchery rep (?), Betsy?


  • Schedule committee meeting
  • Compile list of things I’ll need for the bypass option, plan my attack

from The Shell Game