Tips And Tricks

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

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. Our starting point will be the transcriptomic sequences we used in the differential expression analysis. These sequences must be annotated (Functional Analysis > Blast, Blast2GO Mapping, and Blast2GO

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Retrieve Top Blast Hit

How to change sequence names coming from Prokaryotic GeneFinding?

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

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Generate Venn Diagram

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

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Load Tair Gene Ids from Biomart

Load Sequences/ Annotation from a list of identifiers within Blast2GO

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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Load exon sequences from reference

Load FASTA sequences from Reference and GFF

Sometimes databases provide the whole genome and the GFF or GTF files but not the exon or CDS FASTA files.With Blast2GO it is possible to load Fasta sequences and to extract the exons or the CDS from the genome using the GFF file.

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