I have several assembled, annotated transcriptomes of non-model organisms (fish). I would like to identify what transposons are present in these transcriptomes (LTR, SINEs, LINEs etc) and compare them. I am currently trying to use RepeatMasker to identify them using a clade specific library from RepBase but I was thinking of trying to look for them de novo with REPET. Just looking for suggestions and ideas really. Thank you.
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