Shortish list

Posted by & filed under Ostrea lurida.

In selecting qPCR targets from the Oly transcriptome (version 3) I came up with the following list. In general this was done by first focusing on stress response GO slim terms, followed by simple word searches. The table is available for download here The next step would be some joining & file converting to pull… Read more »

RNA-Seq: Tophat via iPlant

Posted by & filed under Workflows.

Goal: Use RNA-seq to compare expression between oysters (n=3) pre and post heat shock. Based on IPlant Collaborative Tutorial https://pods.iplantcollaborative.org/wiki/display/eot/RNA-Seq_tutorial Task 1: Align read data to Crassostrea gigas genome. Tophat is a specialized alignment software for RNA-seq reads that is aware of splice junctions when aligning to a reference assembly. 1) Click Apps from DE… Read more »