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Old 05-17-2010, 08:34 AM   #1
cliff
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Location: USA

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Default how to check copy number from certain gene

Hi, All

I have a cell mix sample: 30 cells A + 80 cells B. I used Illuima GA to sequence this sample, and then used BWA to do mapping and SAMtools to call SNPs. Now, I want to find how many copies a certain gene has in these two cell lines (i.e., A and B).

Anyone knows a good way to find out the copy number?

I'll appreciate all your help.

-Cliff
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Old 07-14-2014, 02:43 PM   #2
arcolombo698
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I am working on this same issue, did you have any progress here?
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Old 07-14-2014, 03:52 PM   #3
GenoMax
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This tool was just presented at ISMB. http://www.ncbi.nlm.nih.gov/pubmed/25016581 Software is available at: https://oncocnv.curie.fr/
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