How to export Gene Finder GFF output with GO terms?
With the project, I can run the full functional annotation steps Blast, InterProScan, Mapping and Annotation.
Now it would be nice if I could export a GFF file retrieved from Gene Finding containing the GOs from the annotated project.
This is possible with Blast2GO PRO.
How to launch an Enrichment Analysis from pairwise differential expression results in Blast2GO?
It is possible to directly run Functional Enrichment Analysis either GSEA or Fisher Exact Test from a pairwise differential expression analysis executed in Blast2GO.
The list of interesting genes will be generated automatically by Blast2GO and there is no need to create it.
How to create a gene list within Blast2GO to run the functional enrichment analysis?
Blast2GO offers the option to create either single or ranked ID lists depending on the algorithm that will be used for the functional enrichment analysis, the Fisher Exact Test or GSEA.
On one hand, the Fisher Exact Test expects a single column with the sequence identifiers, which have to match the ones with the Blast2GO annotation project.
On the other hand, the GSEA needs a ranked list, where the first column is the sequence identifier and the second one could be e.g the logFC, P-Value of a differential expression project.
How to change sequence name 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.
Generate a Venn Diagram in Blast2GOWhen 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 Blast2GO allows selecting multiple ID lists or ID value lists in text or B2G format to draw the intersection of the elements of the lists.
These ID lists can easily be generated within Blast2GO. It is possible to do all in one place, without the need to go back and forth between Blast2GO and a text editor.
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.
How to load Fasta sequences from a whole genome using a GFF/GTF?
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.
How to rename the sequence name?
Blast2GO allows renaming the name of all selected sequences by converting, replacing or adding text to the actual sequence name.
How to combine two projects in Blast2GO?
Blast2GO allows combining two projects which contain either the same identifiers or different ones.
How to Change the Temp folder Location of Blast2GO
Blast2GO can handle big data, but it needs plenty of free disk space in the systems temporary files folder. If you run into troubles with a shortage of disk space, follow this guide to manually change the location of the folder for Blast2GO temporary files to e.g. another partition.