Sam’s Notebook: Data Wrangling – Rename Pgenerosa_v074 Bismark Coverage Files Scaffold Names

After a meeting today, Steven and Hollie realized that the Bismark coverage files were still using the old scaffold names, stemming from the Pgenerosa_v074 naming. I’d previously updated filenames and scaffold names, so I recycled some of the code used there to rename the coverage files.

The renaming was done in the following Jupyter Notebook (GitHub):

Sam’s Notebook: DNA Isolation and Quantification – Crassostrea gigas and Crassostrea sikamea Mantle Tissue from Marinelli Shellfish Company

Isolated DNA from the C.gigas and C.sikamea samples we received from Marinelli Shellfish Company on 20191030 using DNAzol.

Small amounts of mantle tissue were homogenized using disposable mortar and pestles in 1.5mL snap cap tubes using 500uL of DNAzol. After homogenization, an additional 500uL of DNAzol was added to each sample. Samples were mixed gently by inversion. The manufacturer’s protocol was followed with the following notes/changes:

  • DNA was not spooled; instead it was pelleted per instructions for DNA < 15ug.
  • Initial DNA pellet wash was performed using 70% DNAzol/30% ethanol
  • Final pellets were resuspended in 300uL of nuclease-free water.

NOTE: Most pellets were mostly insoluble (i.e. comprised of “junk” that was carried over). After solubilization attempts via pipetting, the insoluble material was pelleted (5,000g, 5mins).

Samples were quantified using the Roberts Lab Qubit 3.0 and the Qubit dsDNA BR Assay Kit (BR = broad range), using 1uL of each sample.