Sam’s Notebook

University of Washington - Fishery Sciences - Roberts Lab

Posts - Page 2 of 98

qPCR - Relative mitochondrial abundance in C.gigas diploids and triploids subjected to acute heat stress via COX1

  • 2 min read

Using the C.gigas cytochrome c oxidase (COX1) primers (SR IDs: 1713, 1714)I designed the other day, I ran a qPCR on a subset of Ronit’s diploid/triploid control/heat shocked oyster DNA that Shelly had previously isolated and performed global DNA methylation assay. The goal is to get a rough assessment of whether or not there appear to be differences in relative mitochondrial abundances between these samples.

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FastQC and Trimming - Metagenomics (Geoduck) HiSeqX Reads from 20180809

  • 1 min read

Steven tasked me with assembling our geoduck metagenomics HiSeqX data. The first part of the process is examining the quality of the sequencing reads, performing quality trimming, and then checking the quality of the trimmed reads. It’s also possible (likely) that I’ll need to run another round of trimming. The process is documented in the Jupyter Notebook linked below. After these reads are cleaned up, I’ll transfer them over to our HPC nodes (Mox) and try assembling them.

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