Step 1: Preparing and Cleaning Raw FASTQ Reads

The raw FASTQ reads sometimes have adapter sequences and low-quality bases towards the ends, which need to be removed.

We will use Miniconda ( https://docs.anaconda.com/miniconda/install/ ) that has already been installed on the server. Miniconda will help us install and manage multiple software packages.

source /data/miniconda3/bin/activate
/data/miniconda3/bin/conda init --all

📝 Task 1: Obtain a summary of FASTQ files. Count the number of reads in the FASTQ files, and examine the distribution of read lengths and quality.

📝 Task 2: Trim the raw FASTQ reads to remove adapter sequences and low-quality bases from the ends.

Extra note

To install Miniconda ( https://docs.anaconda.com/miniconda/install/ ) from scratch, the following steps may be performed on a different server.

For Linux systems

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

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

source ~/miniconda3/bin/activate

To initialize Conda on all available shells, run the following command:

miniconda3/bin/./conda init --all