Step 1: Preparing and Cleaning Raw FASTQ Reads

The raw fastq reads sometimes have adapter seqeunces and there are low quality bases towards the ends which needs 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 mupliple and manage multiple softwares

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

📝 Task1 : Obtain summary of fastq files. Count the number of reads in fastq file, the distribution of read lengths and quality

📝 Task2: Trim the raw fastq reads to remove adapter sequences and low quality bases form the ends

Extra note

To install miniconda (https://docs.anaconda.com/miniconda/install/) from scratch the following maybe done 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