Entering edit mode
3.9 years ago
ddzhangzz
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90
My customer gave me a list of genes with known strand information to check the copy number variation (CNV) using their WGS data. The results of CNV provided the start and end position but not strandedness. I am concerned to link the CNV results with the gene list by ignoring the strandedness. I am wondering what the best practice might be for this issue.
What does CNV has to do with strandedness?
maybe allele specific calling? strandedness indeed sounds weird
But alleles refer to differences between chromosome pairs, strands refer to the same chromosome.
I don't work much with variation so following is thinking aloud. Extra copies of the gene could potentially be translocated to different chromosome though and may be inserted upside down. So consideration of strand could be useful, especially if there is expression happening?
yeap yeap, it is just my best guess of what the topic starter is looking for
CNV should occur on both strands of DNA, so I think it's safe to ignore the strandedness. Am I right?
Yes, DNA is double-stranded and CNVs refer to aberrations of DNA segments.