Dear all,

Recently, I used RepeatMasker to annotate a transcriptome. In fact, I want to use a custom TE library (such as a plant TE library from http://www.girinst.org/repbase/) to annotate my transcriptome.

But I failed to got the same classified table when I run the command

RepeatMasker Athaliana_167_TAIR9 -lib ~/bin/censor-4.2.29/biolib/athrep.ref -pa 8

as the command

RepeatMasker Athaliana_167_TAIR9 -species arabidopsis -pa 8

do.

So, could anyone please help me in solving this problem or give me any advice?

Thank you very much!