I am thus far quite happy with Repeatmodeler2. I though have more of a question on the output than actually an 'issue' with the run of the software. When using -LTRstruct predicted LTR copies are joint into consensus sequences. Based on the output file, LTR copies (LTR) as well as the internal element (INT) are clustered independently and then reported as independent entries in the consensus family output (at least my interpretation). My question is: is it possible to associate the two LTRs to the corresponding INT element to be able to assess the complete LTR element within a genome (LTR->INT->LTR). In RepBase, to my knowledge, this is possible as the base name of the element is preserved. Thank you very much for your insights, Cheers Michael
Dear development team,
I am thus far quite happy with Repeatmodeler2. I though have more of a question on the output than actually an 'issue' with the run of the software. When using -LTRstruct predicted LTR copies are joint into consensus sequences. Based on the output file, LTR copies (LTR) as well as the internal element (INT) are clustered independently and then reported as independent entries in the consensus family output (at least my interpretation). My question is: is it possible to associate the two LTRs to the corresponding INT element to be able to assess the complete LTR element within a genome (LTR->INT->LTR). In RepBase, to my knowledge, this is possible as the base name of the element is preserved. Thank you very much for your insights, Cheers Michael