search

abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
Other
209 stars 66 forks source link

From normalized_RD to real copy number #153

Closed hoonghim closed 5 years ago

hoonghim commented 5 years ago

Dear professor Alexej Abyzov,

Hello, I am worried that I might have made a mistake in the process of calculating a copy number.

When I get the result of normalized_RD, I estimated the real copy number by rounding the product of normalized_RD and 2 (i.e, round(normalized_RD * 2))

Is this process wrong?

I just read these questions but couldn't find the answer (https://github.com/abyzovlab/CNVnator/issues/24) (https://github.com/abyzovlab/CNVnator/issues/69) (https://github.com/abyzovlab/CNVnator/issues/135)

I followed this explanation - normalized_RD -- read depth normalized to 1.

So to obtain the real copy number of all CNV positions, I applied the following calculation method estimated real copy number = round( normalized_RD *2 )

If this could make any issue, could you please tell the right way?

I thought that genotyping part is only used for a specific genomic region. image

Thanks in advance for your reply.

Sincerely,

Seung-hoon

abyzov commented 5 years ago

Hi, yes your are doing correct round up to get CN. However, please note, that when do genotyping the output is estimated CN. So, you don’t need to multiply by 2.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

On May 16, 2019, at 9:57 AM, hoonghim notifications@github.com<mailto:notifications@github.com> wrote:

Dear professor Alexej Abyzov,

Hello, I am worried that I might have made a mistake in the process of obtaining a copy number.

When I get the result of normalized_RD, I estimated the real copy number by rounding the product of normalized_RD and 2 (i.e, round(normalized_RD * 2))

Is this process wrong?

I just read these questions but couldn't find the answer (#24https://github.com/abyzovlab/CNVnator/issues/24) (#69https://github.com/abyzovlab/CNVnator/issues/69) (#135https://github.com/abyzovlab/CNVnator/issues/135)

I followed this explanation - normalized_RD -- read depth normalized to 1.

So to obtain the real copy number of every CNVs, I applied the following calculation method estimated real copy number = round( normalized_RD *2 )

If this could make any issue, could you please tell the right way?

I thought that genotyping part is only used for a specific genomic region. [image]https://user-images.githubusercontent.com/42195952/57868744-866b5f80-783e-11e9-8b32-4be6a73dc0d9.png

Thanks in advance for your reply.

Sincerely,

Seung-hoon

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/abyzovlab/CNVnator/issues/153?email_source=notifications&email_token=ACLKGOLYJBIUYYZ2JDQ3VUDPVV75FA5CNFSM4HNN7HQ2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GUGWYDA, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ACLKGOKL54RM5TVSHCXG3YLPVV75FANCNFSM4HNN7HQQ.