Splicing around

Posted by & filed under Cgigas DNA Methylation.

Here I am going to see to what degree I can identify differential splicing events that occur upon acute heat stress with the ultimate goal of determing if there is a relationship with differentiall splicing and DMLs. As the Tophat suite was used for RNA-seq, I will start exploring the cuffdiff output. Note all output… 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 »