Differences

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--- chado [2010/01/14 08:12]
172.26.15.184
+++ chado [2010/05/22 14:19]
@@ Line 1: / Line 1: @@
-====== Chado ======
-Create new T.pava Chr1 Chado database from Chr1 Genbank file. Local version of Genbank file does not work. Downloaded new file from Genbank: NC_001142.gbk
-Convert file to gff using script:
-<code>genbank2gff3.pl</code>
-Create pgsql database.
-<code>createdb --template=chado tparvadb
-psql tparvadb
-chado> SELECT * FROM organism;
-chado> INSERT INTO organism ( abbreviation, genus, species, common_name) VALUES ('T.testus','Test','testus','test');
-chado> \q</code>
-Load gff3 data into database
-<code>gmod_bulk_load_gff3.pl  --dbname tparvadb --dbxref GeneID --organism T.parva --gff T.parva_chr1.gb.gff</code>

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