Monthly Archives:: January 2015

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 »