Project Summary: Maturation processes in the marine mollusc, Panopea generosa

Posted by & filed under Panopea generosa.

Work Accomplished The overall goal of this project is to develop a fundamental understanding of processes controlling marine mollusc reproductive maturation. In order accomplish this goal the specific research objectives of this proposal were to 1) characterize tissue specific transcriptomic resources for the geoduck and 2) identify proteins that play a role in geoduck reproductive… Read more »

The Little Things

Posted by & filed under Miscellaneous.

Getting back into gear, I am assisting Andrew ID some targets from a salmonid transcriptome. With said transcriptome I am taking the blast output and getting some protein names sans SQLshare. The tldr can be seen here, but if you have the time I will point out the key code aspects and leave you with… Read more »

pyrad workflow SNPit

Posted by & filed under Snippit.

Working through the GBS data, I wanted to leave a trace of a workflow that will be improved upon (I used the wrong cut site) as well as results for comparison. Only one end of the 96 files (ie samples) was used. Here is the notebook and output directory. Requisite screenshot:

Genes (RNA-Seq) on Oly Genome

Posted by & filed under Ostrea lurida.

We currently have a version (0.0.2) of the Ostrea lurida genome on CoGe. This is 38 scaffolds greater than 80k bp. Below is an effort to map gonad RNA-seq data to said genome. Two male gonad and two female libraries were mapped to the genome using TopHat in Cyverse Discovery Environment. Through the steps… I… Read more »

CoGe on Fidalgo Sibs

Posted by & filed under Ostrea lurida.

As per this pipeline I will run the 8 individuals in the environmental epigenetics mini-experiment. — Once complete this is all available in the genome browser

Fidalgo offspring at two locations

Posted by & filed under Ostrea lurida.

We carried out whole genome BS-Seq on siblings outplanted out at two sites: Fidalgo Bay (home) and Oyster Bay. Four individuals from each locale were examined. A running description of the data is available @ I need to look back to a genome to analyze this. We did some PacBio sequencing a while ago…. Read more »

Getting back on tracks

Posted by & filed under Panopea generosa.

Yesterday I uploaded v0.0.1 of the Geoduck genome to CoGe. Now I want to start adding tracks. To do this I used CLC to create RNA-seq tracks from our male and female gonad transcriptome data. As would be expected only a small amount of reads mapped. This is as we are limiting the genome to… Read more »

Panoplea of data

Posted by & filed under Panopea generosa.

We have had the data for a draft genome of Panopea generosa for a bit. Here is a quick look. All raw data is available @¬† With a first pass assembly here. There are over 14 million scaffolds at this point with 22 scaffolds greater than 100,000 bp. We are using those to kick the… Read more »

Bringing Ocean Acidification System online

Posted by & filed under Miscellaneous.

I was out at Manchester yesterday to help Laura out with getting things going. tldr- Water is flowing, rising temperature seems to be an issue. This could be attributed to air temp and/or pumps. When we arrived water temperature was up to 19C after about a week. We decided to drain down system refill, calibrate… Read more »