Aug. 13-14, 2019, Salmon-Sea lice analysis and geoduck project

Sea lice and Salmon data

Start full alignments using pre-determined settings on Mox
- Created scripts:
  - Salmon: 20190814_BmrkSsalar.sh
  - Sea lice: 20190814_BmrkCalig.sh
- Started running 20190814_BmrkSsalar.sh @ 11:40am
  - takes about 4.5-5 hours/sample so alignments should be done in ~4-6 days including rest of analysis (we’ll see).

copy data from Ostrich desktop to Gannet

note: this is the same data as was copied to Mox /gscratch/scrubbed/strigg/TRIMG_adapt_5bp (see this post)

 	rsync --archive --progress --verbose * /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190806_TrimGalore/ 

  rsync --archive --progress --verbose /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/ strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190806_TrimGalore

copy data from Mox to Gannet

  rsync --archive --progress --verbose /gscratch/scrubbed/strigg/analyses/20190809_100K_Calig_trimG strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/analyses/
	
  rsync --archive --progress --verbose /gscratch/scrubbed/strigg/analyses/20190809_100K_Salmo strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/analyses/
	
  rsync --archive --progress --verbose /gscratch/scrubbed/strigg/analyses/20190809_100K_Salmo_trimME strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/analyses/
	
  rsync --archive --progress --verbose /gscratch/srlab/strigg/jobs/ strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/mox_jobs/

Geoduck Broodstock conditioning manuscript

Go through water chem (nov 2018- mar 2019)
- Apex data:
  - 11/21 - 2/1 here
  - 2/1 - 3/17 need to download
- Discrete measurments here
- Titrator:
  - 11/28 - 1/14 here
  - 1/21 - 3/19 here
- NEED TO:
  - Run cumulative R analysis of all titrator data
  - Consolidate all data into one table
Go through survival data of var. low pH animals
- data here
- analysis here
Go through respirometry data and see if it’s usable
- respirometry data is from Broodstock exposed to constant low pH
Write all in methods and results of manuscript
- manuscript draft here
- paper repo here

Oyster proteomics manuscript

decide on journal
continue comparing results to literature