Ensembl data load
From genomewiki
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