Switching RepeatMasker off in Maker-P
Entering edit mode
7.5 years ago
mafireyi ▴ 80


I am annotating a new plant genome and using the Maker-P pipeline. I have created a custom library using RepeatModeler and the assembled genome and used RepeatMasker to softmask the genome. I want to use this masked genome as input in Maker and not re-do the RepeatMasking. My question is, is it possible to switch off RepeatMasker in Maker and also is it advisable.


Assembly • 3.1k views
Entering edit mode
7.5 years ago
wjidea ▴ 50

If you have the repeat mask features prepared in a GFF file, you can just load to MAKER-P in the maker opt control file and then turn off the repeat mask step in MAKER opt control file.

rm_gff= #pre-identified repeat elements from an external GFF3 file

Entering edit mode
6.1 years ago
Morgan S. ▴ 90

Hi, I have a similar question.

I already masked my repeats using RepeatMasker, so I wanted to include these in Maker instead of having Maker re-do the masking. Would my file opts look like this?

-----Repeat Masking (leave values blank to skip repeat masking)

model_org= #select a model organism for RepBase masking in RepeatMasker rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker repeat_protein=/home/apps/maker/2.31.9/data/te_proteins.fasta #provide a fasta file of transposable element proteins for RepeatRunner rm_gff=/work/Geomicrobiology/msobol/IODP_329_SPG/1371E14H2/repeatmasker/1371E_14H2_contigs.fasta.out.gff3 #pre-identified repeat elements from an external GFF3 file prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no softmask=0 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)

It says to leave everything blank if you want to skip repeat masking, so I wonder how that worked if you include a file in rm_gff?

Thanks, Morgan


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