Goals - June 2015

Before we check out this month’s goals, let’s have a quick review of last month’s goals and which, if any, I was able to accomplish.

From May 2015:

Geoduck Reproductive Development Transcriptomics

Goal(s): Isolate RNA from geoduck histology blocks

Status: Accomplished!

BS-Seq Illumina Data Assembly/Mapping

Goal(s): Glean additional info about this data set and our ability/inability to create our own BS-seq libraries.

Status: Still a mystery. Currently reaching out to Doug Turnbull at the Univ. of Oregon Genomics Core Facility to see if he can provide any insight as to why our data looks the way it does, which might help us figure out why we’re having such difficulty mapping our reads to the C.gigas genome…

C.gigas Heat Stress MeDIP/BS-Seq

Goal(s): BS-seq Claire’s samples.

Status: Untouched. Is dependent upon whether or not we can successfully create our own high-throughput sequencing libraries (see above).



  • Migrate Wikispaces notebook to this notebook

  • Add to GitHub code pages

  • Flesh out/create README files on server(s)

  • Lab cleanup tasks

  • Assist on Jonathan’s Capstone project


  • Migrate Wikispaces notebook to this notebook - Minimal progress

  • Add to GitHub code pages - Updated “Commercial Protocols”, added wget command for offline notebook backups

  • Flesh out/create README files on server(s) - No progress

  • Lab cleanup tasks - No progress

  • Assist on Jonathan’s Capstone project - Things still not working. Had Jonathan isolate gDNA for proper testing of primers.

Geoduck Reproductive Development Transcriptomics

This project is progressing relatively smoothly. Finished RNA isolations from all samples and checked their qualities via Bioanalyzer. Steven and Brent selected samples of males and females to pool for RNA-seq. Goal is to have these two pools sent off to GENEWIZ, Inc. for RNA-seq. Currently awaiting a quote adjustment as well as an answer regarding sample quantity requirements. Hope to have these sent off later today and data back by the end of the month. This data will be used alongside proteomics data that Emma is currently generating.

BS-Seq Illumina Data Assembly/Mapping - C.gigas larvae OA

The troubleshooting for the data from these “homemade” libraries continues. We’ve tried various approaches to trimming the data, but Steven’s mapping attempts are still not yielding great results. I’ve contacted Univ. of Oregon Genomics Core Facility to see if they can provide insight, but haven’t gotten a response. Will hit them up again to see if I can get a response (and some help).

Geoduck & Olympia Oyster Genome Sequencing

We have quotes from BGI Americas for genome sequencing for both of these organisms. Currently, we’re awaiting for funding to be processed, but expect it to be available this month. Hope to send out samples this month.

C.gigas Heat Stress MeDIP/BS-Seq

This is still dependent upon our ability to make our own BS-seq libraries. Until, then, this project will likely be on the back burner for awhile.


I’d like to continue to contribute to our GitHub code repository with various command line tips and tricks. Additionally, I do need to actually spend some time creating/updating README files for our servers. We have a ton of folders that need some sort of descriptor file in them so users know what to expect to find in those folders. Additionally, we have a ton of data that needs descriptions and/or links to the projects from which the data was generated to serve as a means for people to know how/why/from what the data was generated. This has been done for newer data sets, but there’s a tremendous amount of data sets that have no information about them available in the README files. Also along the data management front, I’d like to tackle a bit of a reorganization, particularly re-establishing the go-to resource for lab members to find “stuff.” For example, Jake recently needed to know where/if we had some software and had to ask about it. Better organization on our part would eliminate him wasting time trying to track down this sort of thing. Part of the organizational issue is that we’ve partially transitioned over to using GitHub instead of Wikispaces. However, the transition hasn’t been fully realized/implemented and the result is fragmentation and confusion on where to find lab info. Oh, one last “digital” note. I’ll be teaching the Unix Shell lesson at Software Carpentry on June 25 - 26, so I have to get prepped for that (not on work time, of course).

In the lab, I still need to tackle some lab cleanup tasks that I neglected to deal with last month (autoclaving, glass disposal). Additionally, I need to continue helping Jonathan with his Capstone project, but I need to manage my time with him better.