After loading the sequences, the run blast icon is greyed out in OmicsBox, why? It is possible to load more than one project into OmicsBox and each project will be displayed in a different tab.So to run the analysis on the different projects you will need to have the OmicsBox table active (white tab). In your case, probably the Progress
It is possible to perform a Fisher Exact Test on the 2 groups even if the annotation is in different files (.annot). First, both .annot files (group 1 and group 2) need to be loaded into Blast2GO.The test and reference set have to be generated according to the groups you want to compare. These are normal text files with the
This video shows how to use the ‘Create NCBI GenBank Genome Submission Files’ tool which allows to generate all files (e.g. the Asn1 (.sqn) file) necessary to submit your annotated sequences to the NCBI database. It allows to combine genomic sequences and functional annotations and creates valid GenBank submission files. Additionally, this video explains how to obtain source files (.gff and .annot files), provides
The Time Course Expression Analysis tool allows performing a differential expression analysis of expression data arising from a time course RNA-seq experiment. This application is based on the maSigPro Bioconductor package, which implements a two-step regression strategy to detect genes with significant temporal expression changes and significant differences between experimental groups. This video shows the analysis of count data coming
The OmicsBox Genome Analysis Module allows executing eukaryotic de-novo and RNA-seq based gene finding with Augustus. In this way, it is possible to discover novel, putative coding genes and their genomic positions for yet uncharacterized genome. Based on the Augustus algorithm an ‘ab-initio’ (DNA sequences only), as well as RNA-seq guided (BAM files) gene predictions, are supported. We will
The Pairwise Differential Expression Analysis tool is designed to perform differential expression analysis of count data arising from an RNA-seq experiment. The application, which is based on the software package “edgeR”, allows the identification of differentially expressed genes between two experimental conditions by applying quantitative statistical methods. This video shows the performance of a pairwise differential expression analysis in which
A simple use-case comparing OmicsBox with R chunks for Time Course Expression Analysis The Blast2GO feature “Time Course Expression Analysis” is designed to perform time-course expression analysis of count data arising from RNA-seq technology. Based on the software package ‘maSigPro’, which belongs to the Bioconductor project, this tool allows the detection of genomic features with significant temporal expression changes and
A simple use-case comparing OmicsBox with R chunks The OmicsBox feature “Pairwise Differential Expression Analysis” is designed to perform differential expression analysis of count data arising from RNA-seq technology. This tool allows the identification of differential expressed genes considering two different conditions based on the software package ‘edgeR’, which belongs to the Bioconductor project. This use case shows the basic
The Blast2GO “Translate Longest ORF” tool searches for the longest Open Reading Frame (ORF) in nucleotide sequences and translates them into their protein sequences. You may choose one or multiple of the six possible DNA frames or select the reading frame based on the frame of the best blastx hit. In this video, we will explain how to translate a set of
