Workflow 1: Annotating Oyster Genes

Steven Roberts edited this page Jan 5, 2015 · 3 revisions

This workflow will take focus on taking a simple SQLShare table that has gene IDs and associated expression data and will take you through the steps of figuring out the name, function, etc of each gene.


Initial Data Table: Oyster larvae RNA-seq - OsHV exposure

SCREENSHOT

SQLShare%20-%20View%20Query

https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/solid0078_20091105_RobertsLab_GE_F3%20trimmed%20RNA-Seq.txt


Join with qDOD Cgigas Gene Descriptions Swiss-prot

Select * from
[sr320@washington.edu].[solid0078_20091105_RobertsLab_GE_F3 trimmed RNA-Seq.txt]oshv
left join
[sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]des
on oshv.ID = des.CGI_ID

https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%2540washington.edu/Cgigas%20Larvae%20RNA-Seq%20OsHV&q=

Identifying Expressed Genes Enriched in the Dataset

Select * from
[sr320@washington.edu].[solid0078_20091105_RobertsLab_GE_F3 trimmed RNA-Seq.txt]oshv
left join
[sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]des
on oshv.ID = des.CGI_ID
  
​where UniqueReads >=10​

https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/Cgigas%20Larvae%20RNA-Seq%20OsHV%20UR10


Download file. Corresponding non-redundant SPIDs @ http://eagle.fish.washington.edu/cnidarian/OsHV_larvae_RNAseq_UR10.txt


Joining with GO information (option 1)

Joining https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/Cgigas%20Larvae%20RNA-Seq%20OsHV%20UR10 with https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/qDOD_Cgigas_GO_GOslim_DISTINCT

SELECT * 
FROM [sr320@washington.edu].[Cgigas Larvae RNA-Seq OsHV UR10]ur
left join
[sr320@washington.edu].[qDOD_Cgigas_GO_GOslim_DISTINCT]ds
on
ur.ID = ds.CGI_ID

SELECT DISTINCT
ID,
SPID1,
GOID,
term,
aspect
FROM [sr320@washington.edu].[Cgigas Larvae RNA-Seq OsHV UR10]ur
left join
[sr320@washington.edu].[qDOD_Cgigas_GO_GOslim_DISTINCT]ds
on
ur.ID = ds.CGI_ID

You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.