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:
    • 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:
    • 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
  • Go through respirometry data and see if it’s usable
  • Write all in methods and results of manuscript

Oyster proteomics manuscript

  • decide on journal
  • continue comparing results to literature
Written on August 14, 2019