Annotating RNA-seq alignments to Unigene annotations- is it possible?

Question

[legro.melanie]

Hello Biostars community,

I have aligned RNA-seq data I have to a reference genome assembly for a relatively novel model organism. I used Rsubread to conduct the alignments due to ease and time. Ideally I would like to use featureCounts to complete a rsubread-featureCounts-limma/voom pipeline for a differential expression analysis. However, the only annotations available for this model are Unigene format annotations and featureCounts only accepts GTF/GFF or SAF format files for genomic features.

Has anyone run into this issue before? Does anyone have recommendations of software packages or files conversions for read summarization using Unigene annotations?

I sincerely appreciate any attention and help with this issue!

[GouthamAtla]

Can you show how the "Unigene format annotations" looks like ? I guess you should be able to convert it to SAF format.