Update EXPRESSION_QTLS

logon to phenogen as chornbak

cd scripts/eQTL

depending on the location of the file generated by Laura, you will need to copy it from that location using a command similar to one of the following:

    scp chornbak@stan://Users/chornbak/Downloads/MaxLODsWithCL_BxD_8Sep09.csv .
    scp chornbak@stan://Users/chornbak/Downloads/MaxLODs_Rats_07Oct09.csv .
    cp /home/saba/ForPhenoGen/HXB.BXH.eQTLResults/*.csv .
    cp /home/saba/ForPhenoGen/LXS.Brain.coreTrans/LXS.eQTL.coreTrans.11Mar11.csv . 

Decide whether to truncate or append. Use one of the following commands:

vi eQTL_Mm.ctl
vi eQTL_Rn.ctl
vi eQTL_Exon.ctl  

Then change the file names and the field names

export ORACLE_SID=dev

Use one of the following commands:

./Mm_go 
./Rn_go
./Exon_go

Run this script to see if there's a discrepancy between data in expression_qtls and probesets:

select e.identifier, e.probeset_chromosome, e.probeset_mb, p.chromosome, p.mb 
from expression_qtls e, probesets p
where e.identifier = p.identifier
and (e.probeset_chromosome != p.chromosome or e.probeset_mb != p.mb;

alter table expression_qtls drop column probeset_chromosome;
alter table expression_qtls drop column probeset_mb; 

Go back to Database Update Procedures