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 »

From Ensenada and beyond

Posted by & filed under Panopea generosa.

There have not been many posts recently, but that is not to say I have not been doing any science. Much of what I have been doing is numerous burst commits on the Panopea transcriptome paper / project. This can be found @ You can see all the Jupyter nbs in this sub-directory. I… Read more »

Big day, big clam

Posted by & filed under Panopea generosa.

Today we sampled the geoduck (Panopea generosa) for genome sequencing. Here is how things went down. It was an early morning for the clam, peaking out to see a glorious sunrise on the porch. From there it was off to the lab. After cleaning the surfaces, Brent sampled tissue. We started out started out targetting… Read more »

Second look at Geoduck transcriptome

Posted by & filed under Panopea generosa.

Last week I popped out a quick assembly and annotation on our geoduck gonadal transcriptome. A second assembly was also done using Trinity. Updates August 3 – Confirmed // in file location had no impact on assembly. July 14 – TransDecoder protein annotations 10:40am – added TransDecoder results 10:29am – added Stats via Trinity Output… Read more »