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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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InterProScan with Blast2GO: How to make it work again

Activate development on Blast2GO was discontinued in 2018. All its functionality and more new features are now part of OmicsBox. Because Blast2GO is no longer updated, some of its functions may have stopped working because web services have changed or security certificates have expired, among other things. It is highly recommended to use OmicsBox instead of Blast2GO to benefit from

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Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

1. Introduction Juvenile rhesus macaques commonly suffer from idiopathic chronic diarrhea (ICD). This disease is characterized by inflammation of the colon and repeated bouts of diarrhea. It is a common cause of morbidity and mortality among macaques because it is unresponsive to drugs. The gut microbiome of macaques with ICD is characterized by abrupt changes when compared to healthy individuals.

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New Metagenomics Features

Release OmicsBox version 1.2 (24th of October, 2019) We are happy to announce the following updates for the metagenomics module. New feature include OTU Differential Abundance Testing and several new taxonomy plots: Chao1 Diversity, Rarefaction Curves and PCoA. More details can be found below as well as in the online user manual and Metagenomics Module website. New Taxonomy Statistics and Plots

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BioBam at the 6th Microbiome R&D Forum in Rotterdam

In May, our colleague David Seide attended this year’s Microbiome & Probiotics in Rotterdam, the Netherlands organized by Global Engage. The event is a combination of 3 events, the 6th Microbiome R&D & Business Collaboration Forum, the 3rd Probiotics Congress and the Skin Microbiome & Cosmeceuticals Congress. This global microbiome and probiotics conference series brought together more than 300 industry,

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How to Change the Temp Folder Location for Blast2GO

OmicsBox/Blast2GO can handle big data, but it needs plenty of free disk space in the systems temporary files folder. If you run into troubles with a shortage of disk space, follow this guide to manually change the location of the folder for Blast2GO temporary files to e.g. another partition.

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How to Set Maximum Memory for Blast2GO

OmicsBox/Blast2GO automatically reserves up to 80% of the available system memory (i.e. RAM), which is fine in most cases. However, sometimes and especially on Linux, this can lead to excessive swapping and will slow down Blast2GO. Follow this guide to manually change the maximum amount of memory Blast2GO will be allowed to use.

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