Does the .gtf associated with the WS280 release contain transposons?

I am doing RNA-seq analysis and would like to see if transposon expression changes in my mutant worms compared to wildtype. I would like to know whether the .gtf file found on WormBase (release WS280, PRJNA13758, canonical geneset.gtf) includes annotations for transposons, or whether I would have to manually create my own list (and how I might go about this!) I can’t find any information on WormBase about exactly what the .gtf file includes, so any help would be appreciated! Thank you in advance.

Transposons are not included in the canonical gene set. You can access transposon transcript sequences in FASTA format from the same source as the canonical gene set (WormBase). However, you would need to remove duplicate sequences (b/c transposons are present in multiple copies) from this file to create a minimal set of transposons. You could then align your RNA-Seq data to this minimal set to obtain gene counts (using appropriate thresholds to discriminate matches). Alternatively, you could contact the authors of this study to see if they would share their analysis pipeline. Good luck!

Thank you very much for the reply. I will give that a go and see how I get on!