Question: SNP zygosity from RNA-Seq data (BAM file)
gravatar for ChIP
5.9 years ago by
ChIP580 wrote:


I have a list of SNPs, and I know number of tags covering these SNPs.

What I intend to find further, is whether the SNPs are homozygous or heterozygous from RNA-Seq tag counts.

I have also computed the RNA-Seq tag counts for each of the SNP, like below:

bedtools multicov -bams RNA1.sort.bam RNA2.bam -bed Cordinate.SNP.txt

RNA-seq I have is a paired end.

Could anyone help, in figuring out if these SNPs are homo or heterozygous based upon the RNA-seq tags covering them.

Thank you

rna-seq snp • 2.1k views
ADD COMMENTlink modified 10 months ago by Shicheng Guo8.4k • written 5.9 years ago by ChIP580

You may be able to confidently call a het from RNA-seq data, but I doubt you can do that for homozygous because one copy might be shut off and not expressed.

ADD REPLYlink written 5.9 years ago by Brian Bushnell17k
gravatar for H.Hasani
4.9 years ago by
Freiburg, Germany
H.Hasani970 wrote:

Well, some mutations are of epigenetic nature(e.g. mono-expressed genes). Therefore without a DNA, there is no way of telling whether the original locus is homo or hetero. In the same context, imprinted genes & LOH are another example for what seems on RNA as a mono (please note that these are all different cases).

Moreover, hetero mutations, are not necessarily coming from hetero locus! It could be that the sample is contaminated, or it is an indication for multi-colony sample.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by H.Hasani970
gravatar for Shicheng Guo
10 months ago by
Shicheng Guo8.4k
Shicheng Guo8.4k wrote:

Suppose your reference genome is human, then call SNPs with your RNA-seq data and then compare the called SNPs with your Cordinate.SNP.txt. The accuracy should be evaluated before make further conclusions since imprinted genes and RNA-editing. Later, I will find a data test it and then I can share the accuracy performance

ADD COMMENTlink modified 10 months ago • written 10 months ago by Shicheng Guo8.4k
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