Tips, Tricks and Video Tutorial

Mini-tutorials for common use-cases and to address frequently asked questions FAQs

IsoQuant: Long-Read Isoform Identification and Quantification

  Defining transcript models to characterize isoforms from aligned reads is a crucial step in analyzing transcriptomics data, particularly when dealing with long reads originating from technologies such as Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT). In the past few years, so many algorithms to achieve this task have been published, that it is challenging to keep an overview

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Using BWA for DNA and RNA Alignment in OmicsBox

The Burrows-Wheeler Alignment algorithm (BWA) is a tool designed to align short DNA and RNA reads. BWA is based on the Burrows-Wheeler Transform (BWT), an algorithm designed to rearrange sequences into runs of similar characters to improve data compression and efficient sequence alignment in Bioinformatics. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads

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Differences Between GTF and GFF Files in Genomic Data Analysis

In the field of bioinformatics and genomic research, data representation is a critical aspect that influences the ease and accuracy of analysis. Two common file formats used in genomic data representation are Gene Transfer Format (GTF) and General Feature Format (GFF). While they may seem similar at a glance, there are distinct differences between these two formats that are crucial

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Tips to manage my OmicsBox subscription users

This blog post is dedicated to OmicsBox subscription administrators seeking seamless management of their subscription users. In this quick guide, we will walk you through the various options for adding new users to your subscription and provide step-by-step instructions for managing them through your BioBam account. With OmicsBox, you can update and oversee your subscription online, and as an administrator,

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cutadapt omicsbox

Demultiplexing with Cutadapt in OmicsBox

Barcoding and demultiplexing in high-throughput sequencing experiments Barcoding, or indexing, is a widely used strategy in high-throughput sequencing experiments. This method enables the multiplexing of numerous samples in a single sequencing run by adding a unique DNA sequence to each sample before sequencing. During sequencing, the barcodes are read along with the DNA fragments, allowing the identification and split of

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genetic variaton

Genetic Variation Exploration in Non-Model Organisms with OmicsBox

The study of genetic variation is fundamental in genomics research as it enables the comprehension of mutation causes and effects in the diversity of life. However, research in this field is well-developed in model organisms, while non-model organisms lack sufficient guidance for a consistent variant analysis pipeline. OmicsBox is a robust tool for investigating genetic variation in non-model organisms, facilitating

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OmicsBox Sign-Up Activation Tutorial

In this article, you will find simple and quick instructions to create your OmicsBox account. Please follow each step of the process and in case any doubt or error may arise, email our support team at support@omicsbox.com.   How to Sign-Up in OmicsBox: Step 1: Start Up OmicsBox to activate the software Introduce the Subscription Key you received in your

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OmicsBox won’t start on Ubuntu Linux

On Ubuntu Linux and other distributions, OmicsBox might not start. This can happen due to an incompatibility of JavaFX in combination with Wayland and GTK3. This blog describes a possible workaround for this problem. Step 1: Open a terminal window and check if the following command gives you “wayland”. If it gives you “x11” the OmicsBox is probably not starting

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Generate Gene Venn Diagram Representations with OmicsBox

What is a Gene Venn Diagram? A  Gene Venn Diagram is a graphical representation in the form of overlapping circles widely used to represent relationships among different genes (IDs).  High-throughput sequencing technologies generate large amounts of data sets coming from multiomics studies. At the transcriptomic level, differential expression analysis appears to be a highly important field of study in bioinformatics

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