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diazlab / CONICS

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
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How to check amplification of a specific gene using CONICSmat? #26

Closed biobug16 closed 4 years ago

biobug16 commented 4 years ago

Hi @soerenmueller I just want to check amplification of EGFR in my scRNA Seq data using CONICSmat. Is there a way to check specifically this locus instead of just checking for whole chr7p arm?

Looking for your advice. Thanks.

diazlab commented 4 years ago

The correlation between DNA copy number and average expression level increases with scale. This approach is generally reliable for regions in the megabase scale, but you will not be able to tell the DNA copy number for just 1 gene from RNA sequencing.

From: researchermailto:notifications@github.com Sent: Wednesday, June 17, 2020 11:23 PM To: diazlab/CONICSmailto:CONICS@noreply.github.com Cc: Subscribedmailto:subscribed@noreply.github.com Subject: [diazlab/CONICS] How to check amplification of a specific gene using CONICSmat? (#26)

Hi I just want to check amplification of EGFR in my scRNA Seq data using CONICSmat. Is there a way to check this specifically this locus instead of just checking for whole chr7p arm?

Looking for advice. thanks.

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biobug16 commented 4 years ago

Thank you for the clarification.