After long years of just conceptual knowledge of what the software does, I was dealing with
RepearMasker this week. So, I am not entirely sure I am correct, but this is how I understand it.
The two flags you explored serve for different scenarios:
-species - if the taxa/species is present in the repeat database (
-lib - if you want to give repeatModeler something different.
In your case it seems like your library is completely missing all LINEs, SINEs and a few others. What you can do is to get from the database all repetitions of the corresponding taxa and catinate it with the repeats you are interested in (the one you supplied in the
-lib argument in the first command).
util/queryRepeatDatabase.pl -species Vertebrates > flavoured_vertebrate_repetitions.lib
cat myOwnLibrary.fa >> flavoured_vertebrate_repetitions.lib
RepeatMasker -lib flavoured_vertebrate_repetitions.lib Mygenome.fa
This should produce annotation similar to the bottom case, but also using the repetitions you manually added.
util/queryRepeatDatabase.pl is a script to query the database of repeats and it is shipped together with
-- edit --
The TE classification in the summary file of repeatMasker is based on headers of the repetitive elements in the fasta file you specify in to
-lib argument. So if you want to get the second-table-like, you need to somehow reclassify the repeat library to contan repBase-like classification of TEs. The explanation of lib argument from the manual:
The recommended format for IDs in a custom library is:
>repeatname#class/subclass or simply
In this format, the data will be processed (overlapping repeats are
merged etc), alternative output (.ace or .gff) can be created and an
overview .tbl file will be created. Classes that will be displayed in
the .tbl file are 'SINE', 'LINE', 'LTR', 'DNA', 'Satellite', anything
with 'RNA' in it, 'Simple_repeat', and 'Other' or 'Unknown' (the
latter defaults when class is missing). Subclasses are plentiful. They
are not all tabulated in the .tbl file or necessarily spelled
identically as in the repeat files, so check the RepeatMasker.embl
file for names that can be parsed into the .tbl file.