January 10, 2025
The ABCs of Bioinformatics: Teaching Kids About DNA and Technology
Explaining bioinformatics to a 10-year-old can be both fun and challenging. The key is to use simple, relatable concepts and…
Category: Guides
January 10, 2025
Step-by-Step Guide: Understanding and Redefining the CIGAR String in SAM/BAM Format
The CIGAR (Compact Idiosyncratic Gapped Alignment Report) string in SAM/BAM files is a crucial component for representing sequence alignments. However,…
January 10, 2025
Step-by-Step Guide: Sanity Checks for NGS Data
Next-Generation Sequencing (NGS) data requires rigorous quality control to ensure reliability and accuracy. This guide outlines essential sanity checks for…
January 10, 2025
Step-by-Step Guide: Counting Sequences in a FASTQ.GZ File
Counting the number of sequences in a FASTQ file is a common task in bioinformatics. When dealing with compressed FASTQ…
January 10, 2025
Step-by-Step Guide: Thinking in Parallel for Bioinformatics
Parallel computing is essential in bioinformatics due to the large volumes of data and computationally intensive tasks. This guide provides…
January 10, 2025
Step-by-Step Guide: Metrics to Describe RNA-Seq Data Coverage
RNA-Seq data coverage is a critical metric for assessing the quality and depth of sequencing experiments. Unlike DNA sequencing, RNA-Seq…
January 10, 2025
Step-by-Step Guide: Understanding Bioinformatics
Bioinformatics is an interdisciplinary field that combines biology, computer science, mathematics, and statistics to analyze and interpret biological data. This…
January 10, 2025
Step-by-Step Guide: Determining a Good Threshold for Log2 Fold Change in Differential Expression Analysis
Determining an appropriate threshold for log2 fold change (log2FC) is a critical step in identifying differentially expressed genes (DEGs) in…
January 10, 2025
Step-by-Step Guide: Trimming Illumina Reads Using Custom Algorithms and Tools
Trimming Illumina reads is a crucial step in preprocessing sequencing data to remove low-quality bases, adapter sequences, and other artifacts.…
January 10, 2025
Step-by-Step Guide: Finding Common Motifs in Sequences
Finding common motifs in sequences is a fundamental task in bioinformatics, particularly for identifying conserved regions in DNA, RNA, or…
January 10, 2025
Step-by-Step Guide: Downloading the PAM50 Gene Set
The PAM50 gene set is a widely used panel of 50 genes for classifying breast cancer subtypes. While the gene…
January 10, 2025
Step-by-Step Guide: Resolving “Out of Disk Space” Issues with Picard Tools
Running bioinformatics tools like Picard can sometimes lead to “out of disk space” errors, even when you have ample storage.…
January 10, 2025
Effective Communication with Non-Computational Biologists: A Step-by-Step Guide
Communicating complex bioinformatics concepts to non-computational biologists (NCBs) can be challenging. This guide provides practical tips and strategies to bridge…
January 10, 2025
Step-by-Step Guide to Merging Multiple FASTQ Files into a Single File
Merging multiple FASTQ files into a single file is a common task in bioinformatics, especially when dealing with data from…
January 10, 2025
Step-by-Step Guide to Using Human DNA Reference Files Without ‘chr’ Prefix
When working with human DNA reference files, you may encounter differences in chromosome naming conventions, particularly the presence or absence…
January 10, 2025
Best Practices for Handling Very Large Datasets in Bioinformatics
Handling very large datasets is a common challenge in bioinformatics. This guide provides a comprehensive approach to managing and analyzing…
January 10, 2025
Why is Academic Software Hard to Install? A Comprehensive Analysis
Academic software often comes with a reputation for being difficult to install. This guide explores the reasons behind this challenge,…
January 10, 2025
Step-by-Step Guide to Obtaining Ancestral Allele Information from the 1000 Genomes Project
Ancestral allele information is crucial for understanding the evolutionary context of genetic variants. This guide provides a detailed protocol for…
January 10, 2025
Ethical Issues in Bioinformatics: A Comprehensive Guide
Bioinformatics, the intersection of biology and computational science, has revolutionized our ability to analyze and interpret biological data. However, with…
January 10, 2025
Step-by-Step Guide to Managing and Transferring Large NGS Data
Next-Generation Sequencing (NGS) generates massive amounts of data, often in the form of FASTQ files, which can be several gigabytes…