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 »