quantify RNA isoforms with one nucleotide difference

Question

[db_chrisa]

Hi all,

i am new to biostar and to the genomics field.

i have some RNAseq samples form heterozygous wt/N cells. The difference between the wt/wt and the wt/N is a single nucleotide substitution in a specific mRNA (which of course has lots of other effects..) . My question is how can I quantify in my RNA seq samples the RNA from the wt allele and the RNA from the N (mutated) allele. Given they are both expressed in the wt/N samples.

Thank you! Chrisa

[h.mon]

http://www.rna-seqblog.com/tag/allele-specific-expression/

http://www.rna-seqblog.com/tag/differential-allelic-expression/

[GenoMax]

Past threads that would be useful: How to calculate allele specific expression from RNAseq data
Tools For Analysis Allele Specific Expression In Rna-Seq Data?
Is It Feasible Look For Allele Specific Expression Of Rna-Seq Data When The Dna Sequence Is Not Known