Tips, Tricks and Video Tutorial

Introduction Working with large FASTA and FASTQ files is a routine part of modern bioinformatics, but it is rarely a trivial task. Reference genomes, transcriptome assemblies, protein databases, and high-throughput sequencing reads can easily reach tens of gigabytes, making them difficult to inspect, share, or process on standard hardware. Splitting these files into smaller, more manageable parts is often a necessary first step before

  A functional enrichment analysis is the procedure of identifying functions that are over- or under-represented among a set of genes and may have an association with an experimental condition (e.g., phenotype or drug treatment). Obtaining functional profiles for sets of genes helps to gain a better understanding of the underlying biological processes. Two common analyses to test for enrichment

One of the new additions in OmicsBox 3.3 is the non-NCBI taxonomy databases for Kraken2. With this new feature, we provide users with a broader range of options for taxonomic classification, meeting diverse research needs. Taxonomic Classification with Kraken2 Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to DNA reads. It achieves this by examining the k-mers within

In analyzing long-read RNA-sequencing data, defining a custom transcriptome by identifying novel isoforms is a complex yet essential task that can have far-reaching consequences for any downstream analyses. As long reads allow researchers to examine isoform diversity in significantly greater detail than short reads, long-read sequencing often reveals a large variety of isoforms not yet present in reference annotations, even