Thanks for your attention.
I am constructing a repeat library for a genome sized ~970 Mb.
Firstly I used repeatmodeler to generate a de novo repeat consensus library (libA.fas).
At the same time, I used ltr_struc and ltr_finder to generate a LTR sequences library (libB.fas).
Then I cat libA.fas, libB.fas, RepBase library and another library from MIPS to one file (LIB.fas).
But I get a wired result.
When I used LIB.fas as a input for "-lib" option of repeatmasker, I got 24.45 % region masked in the genome.
While when I used libA.fas (output of repeatmodeler) as a input library, I got 47.78 % region masked.
Can anyone tell me why I used a smaller library to get a larger repeat region masked?
There are some parameters different between two runs, but I can not decide which one could cause this large difference.
Thanks a lot!
My command for repeatmasker is :
for libA.fas:
RepeatMasker -pa 10 genome.fa -no_is -nolow -norna -lib libA.fas
For LIB.fas:
RepeatMasker -lib database/LIB.fas -xsmall -no_is -nolow -pa 10 -frag 4000000 -a -gff genome.fa >Rmask_genome.out
I am constructing a repeat library for a genome sized ~970 Mb.
Firstly I used repeatmodeler to generate a de novo repeat consensus library (libA.fas).
At the same time, I used ltr_struc and ltr_finder to generate a LTR sequences library (libB.fas).
Then I cat libA.fas, libB.fas, RepBase library and another library from MIPS to one file (LIB.fas).
But I get a wired result.
When I used LIB.fas as a input for "-lib" option of repeatmasker, I got 24.45 % region masked in the genome.
While when I used libA.fas (output of repeatmodeler) as a input library, I got 47.78 % region masked.
Can anyone tell me why I used a smaller library to get a larger repeat region masked?
There are some parameters different between two runs, but I can not decide which one could cause this large difference.
Thanks a lot!
My command for repeatmasker is :
for libA.fas:
RepeatMasker -pa 10 genome.fa -no_is -nolow -norna -lib libA.fas
For LIB.fas:
RepeatMasker -lib database/LIB.fas -xsmall -no_is -nolow -pa 10 -frag 4000000 -a -gff genome.fa >Rmask_genome.out
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