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QC II: Quality check
The first thing to do when you receive data is to check its quality and the composition of the sample. There are different tools for doing so, so let's try a couple.
FastQC is a program that generates general statistics from high throughput data (and pipelines). It creates an HTML report.
Create a directory called Fastq
Within this directory, create a soft link to the samples you will be analyzing. Soft links are a special type of files that serve as a reference to another file or directory, this will avoid having several copies of the same data, saving space. Just have in mind that some programs do not work with soft links:
ln -s file1 link1
Create a directory called FastQC
Run FastQC on your samples. (Remember that you can run any tool using -h to check how to run it):
fastqc -h
Once you are done, inspect the html files and fill in this table.
As you noticed, it is a little tedious to inspect every output file one by one. MultiQC is a tool that summarizes different types of analysis into a single report.
Run multiqc -h to know how to run the tool. Run it and inspect the output file .
Q. What type of data was sequenced? What do you think about the overall quality?
Previous: QC I: Intro
Created by Marcela Dávila