Category: Guides

This guide provides instructions to set up, explore, and visualize SAM/BAM files using tools like samtools, IGV, and Tablet, as…

This guide will clarify the differences between FPKM, raw counts, and RPKM in RNA-seq analysis, explaining when and how to…

This step-by-step guide will help you comprehend the output of samtools view. The guide covers essential details about the fields…

Differential Expression (DE) refers to the process of identifying and analyzing genes whose expression levels vary significantly between different biological…

Analyzing imputed GWAS data involves several steps, including quality control (QC), association analysis, and interpretation of results. Below is a…

Introduction FASTA files (.fasta, .fa, .fsa) are commonly used in bioinformatics to store nucleotide or protein sequences. The .fa extension is just a shorthand…

Install Local BLAST in Ubuntu Step 1: Update Your System Before installing any software, ensure your system is up-to-date: bash…

To convert chemical SMILES strings to IUPAC names, several open-source and freely available tools can be used. Below is a…

Several databases curate RNA-Seq data, which can be useful for analyzing gene expression in various biological contexts, such as cancer…

In RNA-Seq analysis, duplicated reads can arise from different sources, and whether to remove them is a debated issue. This…

To disable the reverse complement strand search in BLASTn, you can use the -strand option, which controls which strand of…

If you have a list of Entrez IDs and want to convert them into gene names, there are various methods…

Here’s a comprehensive guide to tools and software for phylogenetic tree visualization, focusing on large datasets. This includes recommendations for…

Parsing large FASTQ files requires memory-efficient and computationally optimized methods. Below are step-by-step instructions using various tools and programming languages…

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”,…

Introduction to Ka/Ks Ratios The Ka/Ks ratio, also known as the dN/dS ratio, is a widely used metric in molecular…

1. Introduction Venn and Euler diagrams are powerful tools for representing logical relationships among datasets. However, plotting diagrams for more…