January 2, 2025
Databases Available for RNA-Seq Datasets
Several databases curate RNA-Seq data, which can be useful for analyzing gene expression in various biological contexts, such as cancer…
Category: bioinformatics
January 2, 2025
Should We Remove Duplicated Reads in RNA-Seq?
In RNA-Seq analysis, duplicated reads can arise from different sources, and whether to remove them is a debated issue. This…
January 2, 2025
Turn Off Blast Search On Reverse Complement Strand In Blastn
To disable the reverse complement strand search in BLASTn, you can use the -strand option, which controls which strand of…
January 2, 2025
How To Convert List of Entrez IDs Into Gene Names
If you have a list of Entrez IDs and want to convert them into gene names, there are various methods…
January 2, 2025
Best Programs for Phylogenetic Tree Visualization of Large Datasets
Here’s a comprehensive guide to tools and software for phylogenetic tree visualization, focusing on large datasets. This includes recommendations for…
January 2, 2025
How To Efficiently Parse A Huge Fastq File?
Parsing large FASTQ files requires memory-efficient and computationally optimized methods. Below are step-by-step instructions using various tools and programming languages…
January 2, 2025
Creating a Volcano Plot from DESeq2 Analysis
Step-by-Step Instructions 1. Install Required Packages Ensure the following R packages are installed: R Copy code install.packages(“ggplot2”) install.packages(“ggrepel”) if (!requireNamespace(“BiocManager”,…
January 2, 2025
Best Practices and Top Software for Calculating Ka/Ks Ratios
Introduction to Ka/Ks Ratios The Ka/Ks ratio, also known as the dN/dS ratio, is a widely used metric in molecular…
December 31, 2024
Step-by-Step Guide: Creating Venn/Euler Diagrams for Six or More Sets in Bioinformatics
1. Introduction Venn and Euler diagrams are powerful tools for representing logical relationships among datasets. However, plotting diagrams for more…
December 31, 2024
Splitting Paired-End SRA Files into Two Correct FASTQ Files
Introduction Paired-end sequencing is widely used in next-generation sequencing (NGS) to generate reads from both ends of DNA fragments, providing…
December 31, 2024
How to Download All SRA Samples at Once: A Comprehensive Guide
This guide is designed to provide a detailed and structured manual for downloading all SRA (Sequence Read Archive) samples associated…
December 31, 2024
Understanding Chimeric Reads
1. Introduction to Chimeric Reads Chimeric reads are sequencing reads that align to two or more distinct genomic regions, often…
December 31, 2024
Single-End and Paired-End Sequencing in Next-Generation Sequencing (NGS)
Introduction Next-Generation Sequencing (NGS) has revolutionized genomic research by enabling rapid and high-throughput sequencing of DNA and RNA. Common platforms…
December 29, 2024
Emerging and Evolving Research Areas in Bioinformatics:
In the fast-paced world of bioinformatics, staying informed about the most relevant and promising research areas is crucial, especially for…
December 29, 2024
Difference Between CDS and ORF: A Beginner’s Guide to Bioinformatics
Introduction In bioinformatics and molecular biology, understanding the difference between CDS (Coding Sequence) and ORF (Open Reading Frame) is essential…
December 29, 2024
Survival Analysis with Gene Expression in Bioinformatics: A Beginner’s Guide
Introduction Survival analysis is a powerful statistical tool used in bioinformatics to understand the relationship between gene expression data and…
December 29, 2024
10 Essential Tips to Master Linux Quickly for Bioinformatics Success
Getting Up to Speed on Unix for Bioinformatics 1. Introduction to Unix Why Learn Unix? Unix is the backbone of…
December 29, 2024
Step-by-Step Guide: Understanding STAR, Kallisto, and Salmon in RNA-Seq Data Analysis
RNA sequencing (RNA-Seq) is a powerful technique for studying gene expression. To analyze RNA-Seq data, bioinformaticians use tools like STAR,…
December 29, 2024
Essential Tips to Kickstart Your R Learning Journey
This step-by-step manual is tailored for beginners in bioinformatics who are looking to dive into R programming. R is a…
December 29, 2024
Mastering Bioinformatics: 100 Must-Read Classical Papers and Why They Matter
What Are Classical Papers in Bioinformatics? Classical papers in bioinformatics are landmark studies or reviews that have profoundly shaped the…