We’ve generated some paired random nucleotide data as gzip FASTQ using nucgen. These will be used to demonstrate the functionality of bqtools.

Let’s take a look at what files we now have:

Type ls in the command line.

You’ll see a directory ./fastq - let’s take a look at the contents of this directory:

This directory contains 8 files representing 4 different samples, each with a pair of R1 and R2 files.

To get a sense of what these look like, let’s explore the first sample:

You’ll notice that each record is a 4-line block of text:

1. sequence header
2. sequence
3. quality header (usually just a +)
4. quality scores