Ensembl data load

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Load Repeatmasker file

  • Run repeatmasker on a fasta file:
 RepeatMasker -species mouse -qq -dir <full_path_to_output_directory> $HOME/workshop/genebuild/test_seqs/test_sequence_to_repeatmask.fa
  • Create a config file
 [RepeatMask]
 db=repbase
 db_version=0129
 db_file=repbase
 program=RepeatMask
 program_version=3.1.8
 program_file=/path/to/repmasker/RepeatMask
 parameters=-nolow -species mouse -s
 module=RepeatMask
 gff_source=RepeatMask
 gff_feature=repeat
 input_id_type=CONTIG
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