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Tips, Tricks and Video Tutorial

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

Cloud Blast and Cloud Units: How to use resources wisely

Stefan Götz September 30, 2020

This article describes how to run CloudBlast wisely. OmicsBox allows you to perform NCBI Blast searches using a cloud system for high-performance computing. This system runs jobs in parallel and autoscales depending on demand. To control usage we use so-called CloudUnits. These units represent computation time (cpu seconds) on the AWS infrastructure. At the moment only Blast and InterProScan consume

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How to run Blast of the differential expressed genes?

Mariana Monteiro December 10, 2019

It is possible to run Blast only on the differential expressed genes and not on all the data with OmicsBox. One has to select only those sequences that have differential expressed genes in the OmicsBox project.First,  make sure that the name of the sequences in the project match the ones from the differential expression results.

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how to cite omicsbox

How to cite OmicsBox, Blast2GO and all available features

Mariana Monteiro September 24, 2019

OmicsBox should be cited as follows: OmicsBox – Bioinformatics Made Easy, BioBam Bioinformatics, March 3, 2019, https://www.biobam.com/omicsbox In case you run functional annotation pipeline on your data (Mapping and Annotation), then the citation is as it used to be, Blast2GO.This is for the Blast2GO methodology: Götz S., Garcia-Gomez JM., Terol J., Williams TD., Nagaraj SH., Nueda MJ., Robles M., Talon

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Multilocus Sequence Typing MLST Analysis Tool

Carlos Menor July 29, 2019

The Multilocus Sequence Typing Analysis Tool of OmicsBox (MLST) is a nucleotide sequence-based approach of characterizing isolates of bacterial species using the sequences of internal fragments of seven housekeeping genes. This video shows step-by-step how to analyze bacterial sequences with the MLST App in OmicsBox. As input, users can provide either DNA-Seq reads in FASTQ or contigs/scaffolds in FASTA format.

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Select .pal files to Run LocalBlast

How to create a taxonomic mapping file.

Mariana Monteiro July 29, 2019

Create a taxonomic mapping file to Make Blast Database within OmicsBox OmicsBox allows creating a custom database to run Blast locally. The blast algorithm will run on the user’s computer against a database that is installed locally.In order to do so, we have to either download a pre-formatted NCBI database (see tutorial) or format our own database (see this tutorial

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OmicsBox Video Introduction

Stefan Götz July 9, 2019

This 5-minute video provides a brief introduction to OmicsBox. All main features of all modules are introduced. OmicsBox is a bioinformatics Solution to easy your Omcis Data Analysis. Our workflows get you  from raw reads tp insights fast and easy.  The presented modules include Transcriptomics, Functional Annotation and Analysis with Blast2GO, the Genome Analysis Module as well as the Metagenomics

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