Hi @eli
Is the goal to find out which lncRNAs are present and differentially expressed in your RNA-seq data? Or to also perform your own lncRNA discovery to use with DE (or other) analysis?
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Known non-coding genomic annotation could be incorporated into the count/differential expression analysis. And may have already been, but perhaps filtered out – it depends on which annotation features were present in your GTF and used to generate counts.
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For lncRNA discovery (and subsequent DE with your RNA-seq data), you’ll need to create genomic annotation data that contains non-coding genomic feature predictions.
Note that genome annotation tools won’t work for larger eukaryotic genomes when working at any public Galaxy server (the analysis will be too large). Update: you can try now in 2025! And that may not even be necessary as there are several non-coding annotation resources already available for many model organisms. For example, Gencode includes lncRNAs for human and mouse in the complete annotation GTFs, and as distinct GTFs: https://www.gencodegenes.org/
GTN Tutorials https://training.galaxyproject.org/training-material/
FAQ: https://galaxyproject.org/support/
Thanks!