intro-to-galaxy-ngs-sarscov2

Perform Quality Control on Raw Reads

Next Generation Sequencing can produce a large number of reads in each experiment, giving low-cost and in-depth information about the underlying RNA or DNA sample. However, every platform will produce errors (incorrect nucleotides in the sequence). Hence, quality control is an important step in data analysis.

Note: The following steps will walk you through how to run the tools. In each step certain parameters are set. If a parameter option appears on the screen but this tutorial doesn’t mention how to set it, leave it at the default.

Step 1: FastQC

FastQC provides several modules to asses the quality of sequencing data.

The FastQC Slides give an overview of these modules in the context of RNA sequencing data.

Run FastQC

(Optional) Trim adapters and low quality read ends with Trim Galore!

Next: Read Alignment

Previous: Obtain Data