RepeatMasker annotation I collected my own denovo library using many different tools Pipeline (structure-based ) and I updated all the headers corresponding to RepeatMasker format, to obtain Repeat coverage in the genome and .tbl annotation.

when I run repeatmasker the annotation results assume to be Homosapien, where Homo annotation table ( .tbl) is limited as shown below Table (1)

Actually my denovo repeat library consists of more than what is in the table above, example, rolling circles, Copia, Gypsy etc.. 

RepeatMasker -Lib myOwnLibrary.fa Mygenome.fa


Table (1)



My question is how can I run RepeatMasker with my own library using -lib Flag and result like the table (2) below, 

the table below assume to be vertebrates genome, this is my aim. 

RepeatMasker -Species Vertebrates Mygenome.fa


Table (2)



Regards
RepeatMasker comes with a buildSummary.pl script.

You can input the .out file from your RepeatMasker run and there is a flag to enter your species

e.g.

buildSummary.pl -species Vertebrates rmrun.out &gt; mysummary.tbl


In the mysummary.tbl, the summary will not assume your run to be Homo (default).