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). 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/
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Thanks!