Open ishengtsai opened 8 years ago
Hi! How did you load information to GEMINI.db?
First query works for me:
gemini query -q "select synonym from gene_summary where gene='ARTEMIS'" NA12878-1-ensemble.db
A-SCID,FLJ11360,SNM1C,DCLRE1C,SCIDA
A-SCID,FLJ11360,SNM1C,DCLRE1C,SCIDA
For the second query are you sure that this gene exists in annotations? http://useast.ensembl.org/Human/Search/Results?q=CTD-3193O13.9;site=ensembl;facet_species=Human;page=1;perpage=10 The only one I see with the similar name in GEMINI.db is CTD-2021J15.2
I hope this helps. Sergey
Hi,
I tried to retrieve additional information from gene_summary but some information of genes appear missing.
Working example:
gemini query -q "select synonym from gene_summary where gene='ARTEMIS'" db
Another example where gene is in variants but not in gene_summary
gemini query -q "select synonym from gene_summary where gene='CTD-3193O13.9'" db
Hence some variants disappeared when joining the tables. Ideally if gene information is not present the variants should still show with NAs in the gene_summary field. How to get around with this possibility?