Classifying TE-containing RNA-seq transcripts into TE-initiated, exonized, and terminated categories
I have RNA-seq–derived transcripts aligned to the reference genome, and I used RepeatMasker to identify TE-containing transcript regions. I would now like to classify these TE containing transcripts into TE-initiated, TE-exonized, and TE-terminated categories.
What would be the recommended next steps? Has anyone worked on systematic classification of TE-containing transcripts?
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