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Tips, Tricks and Video Tutorial

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

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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metatranscriptomics SortMeRNA OmicsBox rRNA ribosomal removal filtering

rRNA Removal with SortMeRNA in OmicsBox

Introduction RNA-seq data from metatranscriptomics NGS projects contains both coding and non-coding types of RNAs. Before any gene expression or taxonomic analysis, it is important to separate reads in families of messenger RNAs and ribosomal RNAs (rRNAs). SortMeRNA, first released in 2012, is a fast and accurate tool for filtering ribosomal RNAs in metatranscriptomics datasets. The core algorithm is based

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Contaminant Removal with Bowtie2 in OmicsBox

Metagenomics Contaminant Removal with Bowtie

Introduction A common preprocessing step in metagenomics data analysis e.g. working with host-associated studies is to remove the host-related DNA from the sequencing data. This is often referred to as contamination removal. A common approach to isolate host-related reads is performing a read mapping against the host genome. Bowtie2 is the reference tool for this task. Since OmicsBox 2.0 this

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IsoSeq long-read analysis

IsoSeq De-Novo Isoform Discovery with OmicsBox

Introduction The IsoSeq sequencing method produces full-length transcripts using Single Molecule, Real-Time (SMRT) Sequencing. Long read lengths allow sequencing of full-length transcripts up to 10 kb or longer, removing the need for transcript assembly or inferencing. Therefore, unlike traditional short-read methods, IsoSeq provides a more accurate and complete view of gene expression and alternative splicing events. This comprehensive understanding of

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Gene Prediction Augustus OmicsBox

Eukaryotic Gene Finding with OmicsBox

Introduction Given a new genome, one of the first and most important tasks is determining the structure of its protein-coding genes. Ab initio gene prediction algorithms play a critical role because they produce gene structures quickly, inexpensively, and remarkably reliable. In OmicsBox, the Eukaryotic Gene Finding application is based on AUGUSTUS, which is one of the most accurate programs for

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Single Cell Clustering Seurat

Single Cell Clustering With Seurat in OmicsBox

Introduction Single-cell RNA sequencing (scRNA-seq) is a technology that aims to study the expression profiles of individual cells, in contrast with the typical bulk RNA sequencing that analyses the expression of large populations of cells together. scRNA-seq allows the identification of different cell types within the same sample, so it is possible to study tissues with more detail. One of

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