New RRBS geoduck data

First sets of BS data is back and analyzed on CoGe.


#bs, #coge, #geoduck, #rrbs, #sequence

Geoduck Methylation Data came in!…

Geoduck Methylation Data came in!

Run Emu, run! 16 concurrent BSMap instances maxing out both processors.


Produced a somewhat concise workflow for Proteomic analysis


Prepped some HOBO loggers for…

Prepped some HOBO loggers for deployment and worked on DMP changes

Upgraded Ram on Emu, Graphed, and Comet works!

Almost feels like a productive day. Upgraded Emu to hopefully speed up analyses, graphed the Geoduck transcriptome methylation data, and got Comet working! Next week I hope to get a unified Proteomics pipeline built to make all of that stuff easier.

Comet on Linux. It’s not easy.

Here’s a temp notebook entry for converting .raw files to .mzxml. I’ll have a prettier R notebook with output tomorrow.


  • Sent a cleaned up version of the geoduck proteomics paper to coauthors for comments/concerns
  • Submitted Heare et al paper:Evidence of Ostrea lurida (Carpenter 1864) population structure in Puget Sound, WA to Marine Ecology journal for review

Oly Samples Summary

Summary of O. lurida Samples

November 2012 – Present (December 2016)

In November 2012, adult oysters from three locations were collected. The three locations became proxies for three “populations”: N (Fidalgo Bay); H (Dabob Bay/Hood Canal); and S (Oyster Bay). They were kept in common conditions at Port Gamble for five months. Then the oysters were out-planted with each population being represented approximately equally at four sites: Northern Site (Fidalgo Bay); Southern Site (Oyster Bay); Hood Canal Site (Dabob/Hood Canal); and Central Site (Manchester/Clam Bay). Each population of oysters were sampled from each site for mortality, growth, and reproductive activity from August 2013 through October 2014. Samples taken during this time can be found in boxes above the refrigerator in FTR Rm 213 and in the -20˚ Merlab in FTR (Jake Heare’s experiment). In Autumn 2015, oysters that were out-planted at the Northern Site (Fidalgo Bay) were taken to Manchester to be used in an experiment (Katherine Silliman’s experiment). Samples from these experiments can be found in boxes above the refrigerator in FTR Rm 213 and in the -20˚ Merlab in FTR. Second generation oysters that were out-planted at Manchester still remain at the Manchester Site (Central Site) and are being used in an experiment (Katherine Silliman F2 experiment). Oysters that were out-planted at the Northern Site (Fidalgo Bay) are still at Manchester as well and will be used in an experiment starting in December 2016. Oysters that were initially out-planted at Hood Canal all died. Oysters that were initially out-planted at Oyster Bay are thought to be at Manchester as well.

Keeping all the names/labels straight:

Populations Out-planting Sites
Location of Origin Alternate names Location Alternate names
Fidalgo Bay N; NF Fidalgo Bay Northern Site
Dabob Bay/Hood Canal H; HL Dabob Bay/Hood Canal Hood Canal Site
Oyster Bay S; SN Oyster Bay/Budd Inlet Southern Site
Manchester/Clam Bay Central Site

Geoduck transcriptome CpG O/E Plot…

Geoduck transcriptome CpG O/E Plot and installing proteomics software



Software install

Finishing up Jake’s paper and looking towards next week’s tasks

Today I am formatting Jake’s paper to Marine Ecology specifications. By Monday, it will be ready to send to the journal.

Next week:

  • BioRxiv proteomics paper
  • Submit paper to Marine Ecology
  • Start oyster seed morphology measurements for Rhonda’s project
  • Finish moving samples from -20˚ in Room 209 to MERLAB so that the -20˚ in Rm 209 can be defrosted