TJGR mCpG and SNPs

./closestBed -d -a /Volumes/web/cnidarian/TJGR_GonadPE_BS_v9_90_CG_5x_50p_METH.bed -b /Volumes/web/cnidarian/MgoTophat_SNP.vcf > /Volumes/web/cnidarian/mCpG_5x50_closest_MgoSNP

Closest

http://eagle.fish.washington.edu/cnidarian/mCpG_5x50_closest_MgoSNP

SELECT * FROM [sr320@washington.edu].[table_mCpG_5x50_closest_MgoSNP]

Where Column17 < 1

http://eagle.fish.washington.edu/cnidarian/mCpG_5x50_overlap_MgoSNP.txt

Run intersect with mRNA

Out of 28k genes

5263 have Methylated CpG that overlap with SNPs

SELECT * FROM [sr320@washington.edu].[table_TJGR_mRNA_intersect_mCpGovSNP]

Left JOIN [sr320@washington.edu].[TJGR_Gene_SPID_evalue_Description]

ON [sr320@washington.edu].[table_TJGR_mRNA_intersect_mCpGovSNP].Column9=[sr320@washington.edu].[TJGR_Gene_SPID_evalue_Description].Column1

https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/mRNA_intersect_mCpGovSNP%20with%20gene%20names

REALLY NEED TO Compare to NON m CpG

or Random selection

or reverse

How mane SNPs overlap with mCPG

./closestBed -d -a /Volumes/web/cnidarian/MgoTophat_SNP.vcf -b /Volumes/web/cnidarian/TJGR_GonadPE_BS_v9_90_CG_5x_50p_METH.bed > /Volumes/web/cnidarian/MgoSNP_closest_mCpG_5x50