Tophat -accepted hits, bam - coverage CDS (percent with all CG) - CV

Sperm 
SELECT Column9, sum(Column14),count(Column14),var(column14),avg(Column14),stdev(column14),min(column14),max(Column14) 
  FROM [sr320@washington.edu].[table_TJGR_MgoTophat_coverage_CDS.txt]  
  Group by Column9


with CV
SELECT * FROM [sr320@washington.edu].[table_MgoTophat_coverage_CDS_summ_cv]


NOW % meth
here is all CG info
SELECT * FROM [sr320@washington.edu].[table_TJGR_mRNA_intersect_allCpG]

From Sperm
SELECT * FROM [sr320@washington.edu].[table_fish546TJGR_mRNA_int_mCpG_2]



Joining 

Select * From [sr320@washington.edu].[table_TJGR_Sperm_Methylation_info_gene.txt]
  Inner join [sr320@washington.edu].[table_MgoTophat_coverage_CDS_summ_cv]
  ON [sr320@washington.edu].[table_TJGR_Sperm_Methylation_info_gene.txt].ID=[sr320@washington.edu].[table_MgoTophat_coverage_CDS_summ_cv].ID












Gill and Sperm

GILL FILE




Find genes that have different gene level % methylation, assess the cv

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Could also take Diff Meth Tiles and across tissue, Examine alternative splicing adjacent




















Gill only 
Check out DH / BBC Tophat