News, Tutorials, Tips and Tricks

End-to-End Analysis of Long Reads in OmicsBox

Long-read sequencing has gained widespread popularity in many areas of biological research due to the many advantages these technologies offer over short reads, as well as the decreasing error rates and costs. Nature Methods named it the method of the year 2022. The field of transcriptomics shows particular interest in long reads, as long-read RNA-sequencing can shed light on the

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Cutting-Edge Long-Read Transcriptomics Research Published in Nature Methods

We are pleased to announce the publication of a comprehensive study in Nature Methods: Systematic Assessment of Long-read RNA-seq Methods for Transcript Identification and Quantification. This research provides an in-depth evaluation of multiple long-read RNA sequencing technologies, comparing their effectiveness in transcript identification and quantification.BioBam participation in this research highlights its expertise in long-read sequencing technologies and its commitment to

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Single Cell RNA-Seq analysis of Arabidopsis thaliana roots

  Single-cell RNA-Seq (scRNA-Seq) analysis has been widely used to investigate animal tissue heterogeneity, principally with human and mouse data. However, this technique is increasingly being used to study plant tissues as well with comparable results. Despite the challenges it faces due to the plant cell wall, researchers have been able to perform single-cell analysis with plant protoplasts, bringing the

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Population Structure Analysis

Population Structure Analysis with OmicsBox

Population structure analysis is a statistical method used to infer the genetic composition and ancestry proportions of individuals within a population. This type of study allows us to understand genetic variation within and between populations. Building admixture models provides insights into evolutionary processes, migration patterns, and even disease susceptibility. ADMIXTURE, now available in OmicsBox, makes this analysis easier by providing a

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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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OmicsBox 3.2 Release

We are happy to announce the latest update of OmicsBox 3.2. “I am particularly happy to announce that with our latest release, our team managed to create a straightforward yet sophisticated solution for the challenging domain of Single Cell Transcriptomics. This marks a significant enhancement to the suite of complex analysis scenarios OmicsBox simplifies, including also Long-Read Transcriptomics, a field

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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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