This will load your data into the Chado database. See perldoc gmod_bulk_load_ for an explanation of the other options this script supports. If you didn't specify this organism when installing Chado, (in response to the question "What is the default organism (common name, or "none")"), then you'll need to add at least the -organism flag to the command. Run the load/bin/gmod_bulk_load_ script from the GMOD distribution: Substitute in the appropriate values for your own organism.
INSERT INTO organism (abbreviation, genus, species, common_name ) VALUES ( 'H.sapiens', 'Homo', 'sapiens', 'Human' ) If you are unsure if this entry exists log into your database and execute this SQL command: You will need to have an entry for your species in the Chado organism table. If you want those to be part of the GFF3 file, you will have to add those manually as well, fixing any non-SOFA feature types. Any skipped features will be printed at the end. If the feature types are not part of SOFA, you will have to hand edit the resulting GFF3 file to change the feature type. It may give several warnings about unrecognized feature types. Note that there's also an older script, don't use it. If you've actually installed BioPerl then the installed script will have been renamed bp_. Use the BioPerl script, found in scripts/Bio-DB-GFF/ within the BioPerl distribution. gff).įiles in the Genbank format have the suffix. This website provides some files in GFF3 format (suffix. A good source for RefSeq files is NCBI's FTP site. First download the Genbank genome files of interest. You can recognize these files by their NC_ and NT_ prefixes.
These steps have been used to load data from genomic RefSeq files.
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