support for transferring miRNA annotations?

[lichennan123]

Hello!

I have been using TOGA lately for transferring hg38 gene annotations to a newly constructed genome and it looks good so far! However, I do notice that annotations for non-coding RNAs such as miRNAs are not applied to my query genome at all, even though my reference genome contains this information and the isoform.txt input includes ensembl gene/transcript ids for every gene type. Do you have any thought about why this might be an issue and what I can do to allow these annotations be transferred? I'd appreciate your advice! Let me know if additional details are needed.

Sincerely,
Chennan

[MichaelHiller]

Right now, TOGA can only handle coding genes, because CESAR is a codon-aware aligner.
We don't have a TOGA version that can project non-coding genes.

If you want to do some coding, you could do the following: For miRNAs that are close to genes or intronic, you could use the aligning miRNA coordinates of the orthologous chain to annotate them in the query.

[lichennan123]

This is very helpful - thank you!