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!
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!
