Sam’s Notebook:

In our various attempts to get the Panopea generosa genome annotated in such a manner that we’re comfortable with (the previous annotation attempts we’re lacking any annotations in almost all of the largest scaffolds, which didn’t seem right), Steven stumbled across GenSAS, a web/GUI-based genome annotation program, so we gave it a shot.

This version of the genome annotation will be referred to as:

  • Panopea-generosa-vv0.71.a2

I uploaded the following to the GenSAS website to potentially use as “evidence files”:

Transcriptome FastA files (links to notebook entries):

TransDecoder protein FastA files (links to notebook entries)

Repeats Files

Sam’s Notebook:

In our various attempts to get the Panopea generosa genome annotated in such a manner that we’re comfortable with (the previous annotation attempts we’re lacking any annotations in almost all of the largest scaffolds, which didn’t seem right), Steven stumbled across GenSAS, a web/GUI-based genome annotation program, so we gave it a shot.

This version of the genome annotation will be referred to as:

  • Panopea-generosa-vv0.74.a3

I uploaded the following to the GenSAS website to potentially use as “evidence files”:

Transcriptome FastA files (links to notebook entries):

TransDecoder protein FastA files (links to notebook entries)

Repeats Files

Grace’s Notebook: September Goals

September

Crab:

  • Keep tabs on data – when it arrives, begin trimming, assembling, annotating process
  • Prepare for PCSGA: take some of what I presented for EIMD 2019, and add more about the research project
  • Interview Genevieve and Shanelle for DecaPod episodes

Oysterseed:

  • Publish raw data and percolator files to PRiDE (once Emma gets back to me)
  • Once that is done and everything is looked over, publish to BioRxiv

Looking back on August:

August post: here

Research

I fixed the crab data sheet and now have a near complete (unsure if I’m missing a few) list of samples used and what was done with them: here

I have been waiting for the sequence data to arrive and have been reading my old posts, and Sam’s old posts related to the next steps. Still haven’t received data.

Outreach

I still haven’t done any of them. Genevieve has been busy, and Shanelle has been working on her RNA extractions. Have plans to get those done this month.

Conferences

I have a list of potential and definite conferences that might be good for me to attend. I have also submitted my title and abstract to PCSGA and will be presenting results for our first assembled transcriptome on September 18th at 4:45pm.

List of conferences of interest:

Conference Location Dates Abstract due
PCSGA Portland, OR 9/17-9/19 submitted
Ocean Sciences San Diego, CA 02/16-02/21 9/11/2019
NSA Baltimore, MD 03/29-04/02
AMSS Anchorage, AK ???

Bolded are ones I’m definitely attending.
AMSS is the one for NPRB, but according to Pam they are only interested in final results… also their website does not say when their 2020 conference will be.

Other:

I cleaned up the RobertsLab/project-crab and my repository for the Oysterseed paper and project, grace-ac/paper-pacific.oyster-larvae.

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