Introduction+to+Galaxy+for+NGS+Analysis

We have created two Galaxy instances in the cloud (that are identical to each other) and we will be working on these instead of the public Galaxy instance.

Navigate to either http://ec2-54-174-40-131.compute-1.amazonaws.com or http://ec2-54-174-48-47.compute-1.amazonaws.com or http://ec2-54-172-140-106.compute-1.amazonaws.com We will be following along with this basic Introductory Galaxy tutorial https://usegalaxy.org/u/aun1/p/galaxy101 (Open this in a new tab so you can follow along)

Exercises: 1) Finding ChIP-Seq Peaks 2) Finding differentially expressed genes
 * Import the **Filtered reads** dataset from **ChIP-Seq Example** Shared Data Library into your history.
 * Import Chromosome 12 hg19 reference fasta from the **ChIP-Seq Example** data library.
 * Import the **ChIP-Seq Example Mapping Steps** from the Shared Workflow list.
 * Run this workflow on the items that you imported into your history (You can run it on just one of the raw datasets or all)
 * Import the **Mapped** shared dataset from the **ChIP-Seq Example** data library and run MACS using Nanog_Rep1_Chr12_Mapped as tag file and Input_Rep1_Chr12_Mapped as control file (you can use default parameters for the rest)
 * Import the **Tophat Outputs** dataset from **RNA-Seq UCDavis 2013 Example Data** into your history
 * Import the **UC Davis RNA-Seq Differential Expression** workflow from the shared workflows.
 * Run this workflow on the tophat outputs to get differentially expressed genes (use 3 replicates for MeOH and 3 replicates for R3G). (Hint: You will need a reference annotation gtf file, which you can find in the Reference folder in the same Data Library)