Mini-tutorials for common use-cases and to address frequently asked questions FAQs
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.
RNA-seq data is sometimes difficult to match with proteins, due to the short length of the reads. When this is the case, it might be useful to try to find EST hits, which can then be used to find new protein matches. In this demo, we will show how to retrieve top EST hits and the different options that this tool
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
A Venn Diagram is a graphical representation of sets or groups of elements or IDs in form of circles where common elements/IDs of the sets are represented by the areas of overlap among the circles. In bioinformatics this is a popular graphical representation to compare subsets, for example when running a pairwise differential expression analysis it might be interesting to
OmicsBox/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.
Sometimes databases provide the whole genome and the GFF or GTF files but not the exon or CDS FASTA files.With OmicsBox/Blast2GO it is possible to load a Fasta sequences and to extract the exons or the CDS from the genome using the GFF file.
