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News, Tutorials, Tips and Tricks

How to run Blast of the differential expressed genes?

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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SPAdes OmicsBox ScreenShot

New Genome Analysis Features

Release OmicsBox version 1.2 (24th of October, 2019) We are happy to announce the following updates for the genome analysis module. New feature includes a new DNA-Seq de novo assembly strategy based on SPAdes.More details can be found below as well as in the online user manual and Genome Analysis Module website. DNA-Seq de Novo Assembly: SPAdes SPAdes (St Petersburg genome

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Busco OmicsBox Screenshot

New Transcriptomics Features

Release OmicsBox version 1.2 (24th of October, 2019) We are happy to announce the following updates for the transcriptomics module. New features include Completeness Assessment and Predict Coding Regions. More details can be found below as well as in the online user manual and Transcriptomics Module website. Completeness Assessment The Completeness Assessment functionality provides quantitative measures for the assessment of transcriptome assembly completeness, based on

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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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A. galli

Reanalyzing the A. galli transcriptomic response to an anthelmintic drug with OmicsBox

In this analysis, we will reproduce the study that was carried out by Michaela M. Martis et al. in 2017 (doi: http://doi.org/10.1371/journal.pone.0185182) with OmicsBox. Introduction Ascaridia galli is an intestinal parasite which infects a wide range of domestic birds. It is especially important in European farms, where it parasites laying hens and cause some economic problems. The only available treatments are

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Metagenomic analysis of two soda lakes, with and without cyanobacterial bloom, with OmicsBox

In this use case we will use the metagenomics tools included in OmicsBox to analyze the microbial communities of two different soda lakes from Brazil. The original study was carried out by Ana P. D. Andreote, et al., 2018 (doi: 10.3389/fmicb.2018.00244). Introduction Soda lakes are special ecosystems found across Africa, Europe, Asia, etc. These lakes show high levels of sodium

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how to cite omicsbox

How to cite OmicsBox, Blast2GO and all available features

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

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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