Hello,
I would love some help with figuring out TE annotations. I'm trying to analyse expression of TEs in bulk RNA- seq data and have come up with a challenge. After converting all the Fbgn to symbols, the TEs seem to have two different annotations? There's ones annotated with Fbti but also in the format like RRxxxxx_transposable_element from RepeatMasker. How do I know which one to analyse?
Thanks so much for the help!!
The Fbti annotations are the curated FlyBase identifiers for specific transposable element loci in Drosophila, so they are the best choice for analysing expression at the individual insertion level in your bulk RNA-seq data. The RRxxxxx_transposable_element labels come from RepeatMasker and denote broader repeat families, which can overlap multiple loci and are more suited to aggregating expression across families rather than precise quantification.
If your counts include both, simply filter for the Fbti ones like this in R:
# Assuming your data frame is 'counts' with a 'symbol' column
te_counts <- counts[grepl("^FBti", counts$symbol), ]
This keeps things straightforward. For family-level summaries, you could map Fbti to families via FlyBase's TE download files if needed.
