Question

How to astimate the copy number of sex chromosome using QDNAseq or other tools (if recomended)

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4.1 years ago

maoxu66 • 0

Hi, I want to ask whether we can estimate the copy number of the sex chromosome. Like QDNAseq, many existing tools choose to ignore the sex chromosome; however, I really need this. Normalization for copy number estimation has pre-hypothesis for diploid; however, sex chromosomes are not. Are there other ways to solve this problem? Thank you!

I use applyfilter(chromosomes=NA), but the result for the Y chromosome is not desirable.

QDNAseq copy number variation • 1.6k views

ADD COMMENT • link updated 2.9 years ago by matrix • 0 • written 4.1 years ago by maoxu66 • 0

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sure, I tried to normalize the read count by median counts, which seems to work fine! Thank you, by the way.

ADD REPLY • link 4.1 years ago by maoxu66 • 0

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Hi, do you solve with this solution? Could you explain please?

thankyou

ADD REPLY • link 2.9 years ago by matrix • 0

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Hi, do you solve with this solution? Could you explain please?

thankyou

ADD REPLY • link 2.9 years ago by matrix • 0

score 0 · Answer 1 · 2020-10-06

If you just need the number of copies of the whole chromosome, simply count the number of reads on chrX and divide by the number of reads on autosomes. You will have distinct clusters of copy numbers.

ClinCNV not only takes into account the sex of the sample, it handles pseudoautosomal regions too (with a flag specified), but it requires around 20 samples or more. https://github.com/imgag/ClinCNV