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:
- I am still copying the output data from mox to gannet, but it will be here:
- 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
Written on February 20, 2019