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 »

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 @¬†http://owl.fish.washington.edu/nightingales/P_generosa/ 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 »