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Mapping of the sample sequence

Alignment of sample sequences against the reference genome is conducted to determine the most likely source of the observed sequencing reads The reference genome is a thorough, well-annotated depiction of …

Interpreting FastQC results

Although warnings or failures in NGS data analysis should be interpreted with caution, they may not necessarily have a detrimental impact on the overall analysis In fact, certain warnings might …

What is a FASTQ file?

The most common raw data output from Next-Generation Sequencing (NGS) platforms is the FASTQ file, which is a text-based format However, depending on the specific technology used, additional files may …

Introduction to the Course Dataset

Dataset for this course The dataset for this course is a benchmark dataset for the WGS analysis of SARS-CoV-2. The Variants of Interest/Variants of Concern (VOI/VOC) lineages study validated a …

Key steps of the analysis pipeline

The DNA-Seq Analysis Pipeline involves a series of steps for processing and analyzing DNA sequencing data It starts with the generation of raw sequencing data through platforms like Illumina or …

DNA Sequencing in the NGS era

NGS refers to a wide range of cutting-edge sequencing techniques used by various platforms The ability to quickly analyse DNA and RNA sequences made possible by these high-throughput sequencing techniques …

Introduction to DNA Sequencing

DNA Sequencing is the process of reading the nucleotides present in DNA: determining the precise order of nucleotides within a DNA molecule DNA Sequencing generally refers today to any Next …

Introduction to software management using Conda

Bioinformatics tools often have complicated dependencies depending on the Operating System Conda, an open-source package manager, helps to curb these limitations. The link below gives a detailed description of Conda …

Progressing in variants exploration

Variants data to explore As a refresher, let’s first review the data we have in hand. We’ve previously seen how to do that for both static or interactive output. # …

Acknowledgments

Acknowledgments Many thanks to all those who were involved in making of the course Bioinformatics for Biologists: Analysing and Interpreting Genomics Datasets Course Lead Educator and Lead Developer Dr Fatma …

Plotting transformation using ggplot2

Advanced plotting options: axis transformation Have you noticed how the previous data we plotted seemed crushed? This is simply because in its default output, ggplot2 optimizes the axis coordinates to …

What next?

What you can do next Free Digital Certificate of Achievement This is a Sponsored course, which means that learners can obtain a free Certificate once they become eligible. To be …

Data visualization using ggplot2

There are many different levels of data exploitation, and visualization constitutes an essential component of this puzzle This is because it: helps interpretation of even complex high-throughput data provides an …

Summary statistics on the data

Before moving to data visualization, there are a few other useful functions and tips you need to know, that will ease the operational analysis of data immensely The number of …