Wed. Feb 20, 2019, Geoduck genome versions, histology scoring, pt. whitney supplies

Geoduck gonad histology scoring:

• worked with Kaitlyn to figure out scoring for geoduck gonad histology
  • we looked at Robert Marshall’s dissertation(he was in the Pearce lab at UBC), Grace’s geoduck gonad project, and Molly’s manuscript (from Brent) for some criteria on scoring .
  • so far, Kaitlyn has recorded the data here
  • for pictures and to find a scope with a ruler for measuring oocyte diameter, I contacted Lindsay in Jackie’s lab to see if we can use theirs.

Collected supplies to bring to Pt.Whitney tomorrow

• heath stacks
• liquid nitrogen in the dry shipper
• pipette tips
• DI water
• Mercuric chloride waste container
• microfuge tube racks (3)
• 1 box large gloves

Comparing alignments with different P.generosa genome versions

• I aligned 4 juvenile geoduck OA RRBS PE datasets to two smaller versions of the P.generosa genome using these scripts:
  • https://github.com/shellywanamaker/Shelly_Pgenerosa/blob/master/scripts/20190214_bmrkPgenrGenm070_10K.sh
  • https://github.com/shellywanamaker/Shelly_Pgenerosa/blob/master/scripts/20190214_bmrkPgenrGenm070_30K.sh
  • https://github.com/shellywanamaker/Shelly_Pgenerosa/blob/master/scripts/20190214_BismarkAlignAS1.2I60_Pgenr070_10K.sh
  • https://github.com/shellywanamaker/Shelly_Pgenerosa/blob/master/scripts/20190214_BismarkAlignAS1.2I60_Pgenr070_30K.sh
• I am still copying the output data from mox to gannet, but it will be here:
  • /web/metacarcinus/Pgenerosa/20190214_10K
  • /web/metacarcinus/Pgenerosa/20190214_30K
• Using the bismark summary files from the 20190214 analyses and the file from 20181101 analysis, I plotted the sample alignments and cytosine methylation info.

• My hunch is that the 30K contig genome is a good middle ground. Entire R analysis here