Quick Introduction

ThorAxe finds s-exons, i.e. potential orthologous exonic regions, and allows the creation of Evolutionary Splicing Graphs (ESG). There are more details in our publication. It offers three programs towards this goal: transcript_query, add_transcripts and thoraxe. The three programs are meant to be run in that order, being add_transcripts optional:

Tip

You can check our YouTube tutorial to see how you can use ThorAxe and visualise the results.

I. Download transcript information from Ensembl

transcript_query downloads the information that ThorAxe needs from Ensembl; it only requires a gene name (as it appears on Ensembl) or an Ensembl stable ID (ENS…). You can find more information on our documentation for transcript_query or by running transcript_query -h. For example, let’s say you want to analyse MAPK8 between human and mouse:

transcript_query MAPK8 --specieslist homo_sapiens,mus_musculus

Tip

As gene names can have synonyms and clashes, it is safer to use the Ensembl stable ID instead. For example: transcript_query ENSG00000107643 --specieslist homo_sapiens,mus_musculus

[OPTIONAL] Add transcripts to the previously download data

If you have transcripts that are not available at Ensembl, e.g. data coming from your experiments, you can manually add them using add_transcripts.

II. Run ThorAxe

Finally, you need to run thoraxe on that data. There are multiple configuration options that you can check in the thoraxe documentation or by running thoraxe -h.

thoraxe -i MAPK8