software related questions

[377079200]

Dear diegozea，
Thank you for providing very useful software.
I would like to know, can the software use the data not from the Ensembl database completely but from the data assembled by myself
with regards

[diegozea]

Hi,

Yes, the software can handle data not from the Ensembl database. You can simply add transcripts from your own experiments using the add_transcripts script. Here are the docs for that: https://phylosofs-team.github.io/thoraxe/programs/add_transcripts.html

Sorry for the delay in getting back to you.

Best regards,

[MarioStanke]

I believe I have the same question and it is not quite answered by the link to add_transcripts, because the input table requires to specify Ensembl gene ids and appears to add to data from Ensembl only.

Suppose, I have only data that is not at Ensembl, say from a disjoint set of species. (How) can I use ThorAxe then?

[elolaine]

Hi,

Thank you for your interest in ThorAxe!

We are currently testing and using add_transcripts to integrate custom transcripts in the ESG. We found several bugs that we fixed, we pushed the new version this morning.

For now, you can use add_transcripts only after a transcript_query run to:

• add custom transcripts from a gene/species already present in the Ensembl data retrieved using transcript_query; for instance, say you retrieved data for gene ENSGXXX and then you add new transcripts for the same gene ENSGXXX. Or,
• add custom transcripts from a disjoint species; for instance, say you retrieved data for gene ENSGXXX and then you add new transcripts for the orthologous gene in Zebra Finch -- in principle you could define a fake Ensembl id if the species is not at all in Ensembl, we haven't tested this thoroughly though.
  You can add custom transcrpts that you assembled yourself, provided that you comply with the required input table format, as specified in the documentation.

Hope this helps, please do not hesitate to reach out to us again if you face difficulties or if you have specific functionalities you would like to see implemented.

[MarioStanke]

Thanks. I didn't understand what data is downloaded from Ensembl. Now I conclude that the table contains all data, in particular, no tree is externally input, right?

[elolaine]

Hi,

The data downloaded from Ensembl are the annotated transcripts and exons (nucleotide sequences, chromosome coordinates, also for coding parts, phase, strand..etc), as well as the gene tree. But this tree is only needed when the –phylosofs optional argument is used: this functionality formats the output of ThorAxe such that it can be used directly by the PhyloSofS method, which reconstructs phylogenetic forests of transcripts. If you're not interested in running PhyloSofS, you do not need the tree.