How to combine pairwise differential expression results with a functional annotation project in OmicsBox?
Once differential expression results are retrieved, it could be interesting to assign functional annotations to the differentially expressed genes and visualize the results in a single project. This is possible in OmicsBox.
This article explains how to export a GFF file with GO terms in Blast2GO.
This article explains how to start functional enrichment analysis of pairwise differential genes in Blast2GO.
This article explains how to create ID lists of either Blast results or differential expressed genes in Blast2GO.
When running GeneFinding the sequences receive a name with the predicted genes. The first part of the sequence identifier comes from the genome reference sequence name (de-novo assembly) and then a _orfx is appended, where x is a number. Sometimes this name is not useful to proceed with downstream analysis or compare results from other experiments. Is there any way
When running a pairwise differential expression analysis, I was interested in rapidly visualise the genes that overlap between KOvsCtrl, TretvsCtrl and KOvsTret comparisons. The Venn Diagram tool offered by OmicsBox allows selecting multiple ID lists or ID value lists in text or .b2g/.box format to draw the intersection of the elements of the lists. These ID lists can easily be
Blast2GO offers two different features to retrieve the gene/protein sequences as well as the corresponding annotation from a list of identifiers within Blast2GO PRO. Both features can be found under File > Load > Load Annotations. The expected input file is a text file with the identifiers in a single column without a header.
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