Ensembl data load

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

• Define the type of analysis

[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

• load the analysis into the mysql database

$HOME/cvs_checkout/ensembl-pipeline/scripts/analysis_setup.pl $DBSPEC -read -file test.ana