Ensembl data load: Difference between revisions
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RepeatMasker -species mouse -qq -dir <full_path_to_output_directory> $HOME/workshop/genebuild/test_seqs/test_sequence_to_repeatmask.fa | 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] | [RepeatMask] | ||
db=repbase | db=repbase | ||
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gff_feature=repeat | gff_feature=repeat | ||
input_id_type=CONTIG | 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 | |||
Revision as of 15:14, 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
- 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
