FASTQ Preprocessing Instructions

Background

The raw FASTQ reads sometimes contain adapter sequences and have low-quality bases toward the ends, which need to be removed before further analysis.

Install Conda

Follow the instructions here: Miniconda Installation Guide.

For Linux Systems

Only run the below commands if Miniconda is not already installed:

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm ~/miniconda3/miniconda.sh

Post Installation

After installing, close and reopen your terminal application, or refresh it by running:

source ~/miniconda3/bin/activate

To initialize conda on all available shells:

miniconda3/bin/./conda init --all

Tasks

• Obtain a summary of FASTQ files.
• Count the number of reads in the FASTQ file.
• Check the distribution of read lengths and quality.
• Trim the raw FASTQ reads to remove adapter sequences and low-quality bases from the ends.