Workflow: Annotating Oyster Genes

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.

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

SCREENSHOT

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

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Join with [qDOD Cgigas Gene Descriptions (Swiss-prot)](https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/qDOD%20Cgigas%20Gene%20Descriptions%20(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

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

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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

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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

​