Test of allele-specific expression by genome and transcritome sequencing

[baohua100]

We sequenced the diploid genome of a single individual and their transcritome.
(Poplar)

Fisrt, we identiy all the heterozygosity SNPs (genome).

If i know it's a heterozygosity SNPs, Should I do a chi square test using the number (65,89,38,28) or do a bionomal test (50,50,38,28) ?

an example of heterozygosity SNP (The numbers are counts of the two alleles observed in gDNA or cDNA)

gDNA cDNA
A 65 38
G 89 28

[townway]

I think bionomal test is better or you might have to say you also detect imbalance in DNA level which is a little bit uncertain

We sequenced the diploid genome of a single individual and their transcritome.
(Poplar)

Fisrt, we identiy all the heterozygosity SNPs (genome).

If i know it's a heterozygosity SNPs, Should I do a chi square test using the number (65,89,38,28) or do a bionomal test (50,50,38,28) ?

an example of heterozygosity SNP (The numbers are counts of the two alleles observed in gDNA or cDNA)

gDNA cDNA
A 65 38
G 89 28