"nan" for squared correlation between prior and posterior genotypes (fSNPs)

natsuhiko / rasqual

Robust Allele Specific Quantification and quality controL

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"nan" for squared correlation between prior and posterior genotypes (fSNPs) #17

Closed gouthamatla closed 5 years ago

gouthamatla commented 5 years ago

Hi Natsuhiko,

I ran RASQUAL on ATAC-Seq data to get the lead SNP per peak. Out of 121,214 peaks I analyzed, 54,232 snps have -nan in the 24th column, Squared correlation between prior and posterior genotypes (fSNPs) . Is it because those SNPs are not fSNPs but rSNPs ?

Thanks, Goutham A

natsuhiko commented 5 years ago

Hi Goutham,

If there is no fSNP within the feature, the 24th column becomes NA.

Best regards, Natsuhiko

gouthamatla commented 5 years ago

Thanks Natsuhiko for quick reply.