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  • Discrepancy between genotype and expressed alleles

    Hi all,

    I am working on the analysis of allele-specific expression using both genotype information and RNA-seq data from the same individuals. I am looking at predefined SNP positions. But recently I noticed something strange. For a small part of the SNPs (around 4000 of 6,5 million) I see that the true genotype does not match the alleles that are expressed.

    For instance, I see the following cases:

    - Genotype is TT, but only C is expressed
    - Genotype is CC, but both C and T are expressed
    - Genotype is AC, but only G is expressed
    etc.

    I guess this can be due to either wrong genotyping or wrong alignment of the RNA-seq reads. Or is there another explanation? I am aware of the phenomenon of RNA-editing, but to my knowledge this holds only for specific changes.

    If you have any idea or solutions how to prevent this, please let me know.

    Thanx!

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