Question: Strandedness of whole genome sequences?
0
gravatar for ddzhangzz
8 weeks ago by
ddzhangzz90
United States
ddzhangzz90 wrote:

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.

next-gen • 156 views
ADD COMMENTlink modified 13 days ago by Biostar ♦♦ 20 • written 8 weeks ago by ddzhangzz90

What does CNV has to do with strandedness?

ADD REPLYlink written 8 weeks ago by ATpoint36k

maybe allele specific calling? strandedness indeed sounds weird

ADD REPLYlink written 8 weeks ago by German.M.Demidov1.8k
2

But alleles refer to differences between chromosome pairs, strands refer to the same chromosome.

ADD REPLYlink written 8 weeks ago by ATpoint36k
1

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?

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by genomax87k

yeap yeap, it is just my best guess of what the topic starter is looking for

ADD REPLYlink written 8 weeks ago by German.M.Demidov1.8k

CNV should occur on both strands of DNA, so I think it's safe to ignore the strandedness. Am I right?

ADD REPLYlink written 8 weeks ago by ddzhangzz90
1

Yes, DNA is double-stranded and CNVs refer to aberrations of DNA segments.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by ATpoint36k
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