Should I Be Concerned About The Discrepancy Between The Results Produced By Repeatmodeler And Repeatscout

Question

[jomaco]

Hi,

I have just run RepeatModeler and it seems to have completed succesfully. The output file from RepeatModeler (consensi.fa.classified) has fewer sequences (861) than when I ran RepeatScout on its own (4356). Should I be concerned about this discrepancy or is it fine to stick solely with the RepeatModeler results?

Although there is no reason to suggest having more sequences is better, RepeatModeler uses RepeatScout so I was surprised to see fewer sequences given that RECON also contributes to the set of repeat motifs.

Thanks.