Ensembl data load: Difference between revisions
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== Load Repeatmasker file == | == 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 | * Create a config file | ||
[RepeatMask] | |||
[RepeatMask] | db=repbase | ||
db=repbase | db_version=0129 | ||
db_version=0129 | db_file=repbase | ||
db_file=repbase | program=RepeatMask | ||
program=RepeatMask | program_version=3.1.8 | ||
program_version=3.1.8 | program_file=/path/to/repmasker/RepeatMask | ||
program_file=/path/to/repmasker/RepeatMask | parameters=-nolow -species mouse -s | ||
parameters=-nolow -species mouse -s | module=RepeatMask | ||
module=RepeatMask | gff_source=RepeatMask | ||
gff_source=RepeatMask | gff_feature=repeat | ||
gff_feature=repeat | input_id_type=CONTIG | ||
input_id_type=CONTIG | * | ||
Revision as of 15:12, 13 September 2010
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
